in the init makes everything work out of the box. The only issue that I had is that I have to define keybindings in a hook that I add as:
(add-hook 'LaTeX-mode-hook 'auctex-keybindings-h)
Everything else e.g. configuration using setq works well out of the box. I used to use the emacs customize functionality but not any more. I remember it also worked correctly. If anything, to have the configuration options loaded and displayed you should open a .tex file first so that the package loads.
I do however remember significant issues with use-package and auctex. It may have been my fault but that is one of the reasons I abandoned use package and decided to use straight and do things manually.
Best,
Gennady
P.S. If you want I can clean up a bit and share a minimal working config. I often do so to prepare a clean emacs when submitting bug reports. Straight.el makes it easy enough
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Gennady Uraltsev