Thanks a lot for the kind words!
I can see the the problem, but it's unfortunately not very straightforward to fix, without at least compromising in some other areas and possibly even breaking existing designs.
If I add an absolute limit to the minimal and maximal length of the muscles, that wouldn't really fix your problem, since the "global" max limit (that applies to all muscles) would have to be much bigger than you want, in case that you do need to use a longer muscle somewhere in your design.
If I use relative limits (e.g I say the muscle can only stretch to 200% of its original length within the design) then that will limit behaviour of your creatures in a lot of designs where you wouldn't expect it. For example, if you had to place two bones together at a small angle, but then wanted a muscle between the two to expand far enough to create a very large angle, the muscle wouldn't be able to do that, which would make it seem like it's not strong enough.
The best way I can currently think of to incorporate this would be to add general options to each individual muscle, where you could adjust stuff like this (relative expansion/contraction limits, force...) on a per-muscle basis. That way I could keep the current muscle settings as a default but also allow you to do some adjustments if you like.
However, that's going to take quite a bit more time to implement as compared to just slapping a fixed, non-adjustable limit on every muscle, and since I currently barely have any time to spend on this project I can't say how long it's going to take me (probably a few months) or if it's going to work out at all - I might come across some unexpected issues and would have to scrap this idea.