Varnish lifting at joint in toe rail etc.

One way is to cut a 3-4 mm distance in the rail. Then you can seal the end grain with oil or varnish, and then use Sika to fill the gap.

Hard to tell without pictures if it's the same phenomenon, but on the big Roamer I ran. the butt joints on the 5" wide toe rails would be the first to delam, turn white, and lift. Found that the problem was failure of the bedding allowing water to wick up into the joint. In that case, I reefed out as much old bedding as I could and created enough space under the toe rail to be able to shoot in a good caulk bead, Having some thickness to the bead is vital, so the material can stretch, move, expand, and contract. Too thin of a caulk bead will sheer.
Another boat I ran had recurring varnish failures at the cap rail to fiberglass hull juncture. On that one, I cured as AMG suggests. Open up the joint and varnish before laying in the sealant. I figured that the visible caulk line was around 3/8" wide anyway, so open it all up and get some good flexible caulk volume in there. I actually cut some teak out of the joint to create space. Problem solved. For a longer time, anyway. All varnish is transitory .

The joints are also affected by temperature change over the season if you stay in the NE. On my Egg I used to check the bedding and varnish all my outside teak as necessary thru out the year. Two coats at least once a year was my regime. In 13 years I never had to strip and redo the varnish from scratch except in a few small areas.

I think this is the answer.
I have had this same issue with varnish, Cetol and Awl bright.
I've heard of cutting the 3mm along the length of the seam and filling it with west system mixed with teak wood dust to look like the wood around it and, in theory, look like the same color.
I have not tried that.
I am at the same cross road with a couple seams, not all of them.

Cutting the butt joint makes sense. Cut some pieces of backer rod to partially fill gap, then caulk.

Doing this right now. Made a jig, routing out a clean gap where the joint separation is located, filling with West System while leaving a small detent, then topping the detent with the same West System mixed with clean sawdust from the rail. Cure, sand, refinish. Looking under the cap rail I see some places that can be sealed up to prevent moisture from wicking up in that area. Curing that as well.

To me, this sounds as going from bad to worse? My idea is to fill the the gap with a flexible product, not a hard one...

That is what i'm thinking, you want to absorb the expansion of the wood.

My take after a couple of failed efforts is NOT that the wood needs to flex, but other that the joint needs to be clean for stabilization. Yes, you could use a GFlex-like epoxy, but I'm trusting that the bond will hold the teak if the moisture is finally locked out.

With the joint gapped, you can seal the ends of the wood cap. All that is needed is a soft caulking material in the joint/gap as a filler that can be removed without too much work. Probably would want to remove the filler material occasionally to reseal ends of wood. Any hard joint/gap filler would crack and maybe break sealer on ends of wood, which would allow moisture to penetrate wood, and is what you are trying to prevent. Thinking a clean caulk line would look ok at the joints.

AMG has the do it once and be done solution. I have had good results with sawing or sharp chisels, depending on the shape. Cut 1/4" x 1/4" with centerline over the joint so that you have clean edges on both timbers. Everyone has their own preference for sealing end grain, mine is Smiths Penetrating Epoxy (2-part). Apply until saturated. I use TDS deck compound in the taped sealed joint and I do this soon as the 2 - part has gassed off. Now you have end grain that will not absorb moisture and a flexible joint. Last one i repaired was 7 years ago and its still working. TDS comes in white, grey, and black, BoatLife or Star-Brite has a teak like color.

If you have a nice fit of those toe boards, I would hurt me deeply to cut a gouge to put in a patch. IMO, take those joints down to bare wood and start you're finish from scratch. It will take some work to get the hue of the teak even again depending on the previous use of stain.