Should I buy a boat with IPS drives?

I don't think it should be necessary to ask anything special to the dealer, actually.
If they repowered the P680 with the 1350 instead of the 1200, by definition the builder must have propped the IPS according to the higher power.
Among other technical reasons, that's also necessary for passing the seatrial check upon commissioning, required by all engine manufacturers to validate their warranty.
The basic rule is always the very simple and old one, also for IPS: the boat, when loaded, must achieve the rated rpm and 100% load.
Speed is just a dependent variable, so to speak.

Btw, the 1350 package is essentially powered by the same engine as the 1200.
In fact, as you surely know, the IPS naming is just a meaningless marketing trick.
What actually powers the 1200 package is a 12.8 liters engine with an output of 900hp @ 2300rpm.
And the 1350 is powered by the very same block, spiced up to produce 1000hp @ 2400rpm instead.
So, with his new P680, what your son in law will actually get is 200 more hp in total, at a higher rpm, and with 700+ additional lbs in the e/room.
Now, I know absolutely nothing about the P680 performances, but having an idea about how much this sort of difference can affect a 70 footer weighing almost 100k lbs when loaded, well, on one hand I wouldn't call it trivial, but I wouldn't hold my breath for a much higher speed either.

In fact, I wouldn't be surprised it the builder should even install on the 1350 some slightly shorter props compared to the 1200, to allow for the additional 100 rpm the engines are rated for.
The 1350 boat could (and should!) still be a bit faster of course, depending on how the prop pitch and the higher rpm combination works out - but not much, I would guess.

Anyway, my whole point is that also with pods, like with shafts or any other transmission, there is no magic propeller that can be used to make the boat go faster, because also pods are constrained by physics as anything else.
What makes a big difference is the well known rule that drag becomes more critical as speed increases, and in an exponential rather than linear manner.
THIS is the reason why pods don't make sense for powering fast boats: at high speed, you don't want two propellers on each side, neither large blades, nor a large diameter hub, not to mention a large chunk of metal - neither in front nor behind props.
As much as you don't want a long shaft spinning and a P bracket, of course.
In this respect, leaving aside waterjets which are more tricky, the comparison with surface transmissions is mind boggling, just by looking at them.

Of course, you can still make also a pod powered boat go fast (up to a point), by just throwing more power at it, but the faster the boat, the higher the drag losses and the lower the overall efficiency.
Btw, that's the same reason why duoprop outdrives on speedboats are totally unheard of.
It's as simple as that.

I don't think the Prestige's are exactly a fast hull or fast boat, so you're better off with the standard props.

LOL, well, that's a way to look at that.
By the same token, it also helps making the fuel burn of 900/1000hp engines appear lower when considered as 1200/1350hp, I suppose...

I don't think they will, and even if they would, I'd expect them to ask you to sign a release of liability agreement.

See, both Twin Disc and ZF engineers could design fixed surface transmissions during their coffee break, if they wanted to.
There are good reasons why the best transmission builders stick to steerable and trimmable transmissions, instead.
What those nice Kiwis are now building is almost identical to what Intermarine experimented at length many years ago, together with Sonny Levi and his so-called LDU (Levi Drive Unit).
But eventually, they didn't exactly flood the market with those boats and transmission, as I'm sure you know.
According to an officer who used to be in command of a patrol boat powered by that system, the boat was quite simply "impossible to maneuver".
But I suppose that less maintenance demanding, those Q-SPD things probably are - I should think so too!

Anyway, best of luck if you would decide to give them a try and Pershing would accept your request.
I for one would be curious to follow the progress of such project, if you would like to keep us updated on it!

Because they are mechanically complex units.
And mechanical complexity doesn't like being permanently submerged in sea water - pretty much as it doesn't with outdrives and IPS.

But they are complex for good reasons.
Fixed surface transmissions are right at the pinnacle of efficiency, if you want to use a boat always at her optimal design speed, optimally loaded, and you don't mind a maneuverability that makes every mooring a big challenge.
It's no coincidence that this is the route Buzzi chose for his 80 footer that broke more records than I can remember (like the Venice-Montecarlo and Round Britain, just to name the most well known).
On top of that, he fitted staggered MTU engines for best weight distribution and to spread the thrust between four of his own design Trimax combo (transmissions+rudders+trim tabs - see below).
As a consequence, the engine room took all the space it deserved, because obviously he couldn't care less about internal amenities.
Now, THAT is a no-nonsense setup designed for one and only purpose, i.e. go fast also in harsh sea conditions, and for very long distances.

Pershings (as well as ABs, PJs, and the likes) are nowhere near so extreme, and while they are indeed designed to be fast, they are neither meant to need a race pilot to helm them, nor to make berthing a scary experience. Not to mention getting rid of gin-palace interiors in favor of tankage and other technical requirements.
But if your son is willing to accept all the compromises that in extreme boats come with the territory, you could get in touch with Otam.
In fact, they now build an 80 and an 85 based on that original Buzzi hull mould (both within the 24m license limit, btw).
Much more civilized actually, with twin Cat C32 on Arnesons (still good for 40+ kts, mind!), because that's more than enough for most folks.
But they might be willing to undertake relevant customizations - within reason, of course.
More than Ferretti Group, I think.

Anyway, your and your son's problem is a very nice one to have, that's for sure.

There aren't really many failures with Arnesons if you exercise them regularly. It's only when they sit. If you work the drives up and down and side to side every 2 weeks, you won't have any issues. When you let barnacles grow on the rams, then seals start failing on everything.