with-emacs.sh VS guess-language.el

Well, this is impossible to test if you don't say on what version of Emacs you're experiencing this. You could test if it is your configuration by using the lovely with-emacs script to sandbox.

Check out https://github.com/alphapapa/with-emacs.sh

FWIW, I would generally recommend using with-emacs.sh rather than chemacs2, because it's much simpler to use: https://github.com/alphapapa/with-emacs.sh

Whenever you encounter weird behavior, you should try to reproduce it in a clean Emacs config. This script makes that easy: https://github.com/alphapapa/with-emacs.sh

Not to poach, but you might try this alternative: https://github.com/alphapapa/with-emacs.sh

Wow, finally! And just when I've gotten the bugs ironed out of with-emacs.sh and makem.sh related to Emacs 28's changes. Well, pre-29 versions will still be around for a long time, so with-emacs.sh will remain useful, but it will be nice to have support for this integrated into Emacs.

Sure, but you don't have to throw away your old, comfortable, known-good config to try a new one. Use with-emacs.sh to run as many Emacs configs as you like.

And about 20 minutes later (native comp with full AOT takes a while), I could just run emacs-28.0.60 (or with my script, with-emacs.sh -e emacs-28.0.60 -d ~/src/emacs/configs/ap.el).

If I understand you correctly, you are talking about some other config (not your main one), that complains about missing third party library (https://github.com/tmalsburg/guess-language.el). The config you try doesn't have to install missing packages itself automatically, although it may do it, and in fact, it doesn't have to use straight.el at all. Hence this has nothing to do with chemacs2, but everything to do with the config itself and its structure. Hence, just install the library yourself in this config, but first of all check which package manager it uses.