Given my limited usage of system themes to one that has flatpak packages (Materia) and tendency to go through the permissions of new flatpaks and tighten them anyway, those are good points to mention. For theming, it is definitely a trouble point depending on the platform and theme used. Especially when combining Qt5/Qt6 apps, Fltk, GTK2,3+, and GTK4 applications together, things may get even more messy than consistent theming on native applications. Having comprehensive theme packages for the theme you use almost completely resolves this problem. Though I doubt predefined customization isn't something that will be popular with some users given that ricing your Linux desktop to the extreme is a huge selling point of the Linux desktop for many.
I did forget about how especially with Flatpak and Snap how there is no actual guarantee that the default sandboxing permissions will actually be any good or even usable on many applications, which is an issue that partially comes from when community maintainers end up publishing packages for developers rather than developers or dedicated platform testers publish a given package (a common practice for many applications on the Flathub repository).
The battery indeed by no means (at least on intel 11th, 12th gen cpus is what I would call exceptional by any means (4-9 hours on a i5 1240p with two USB-A, two USB-C passive modules). Some expansion modules such as the microSD reader can be a detriment to battery life overall as well as some modules (like the older revision of the HDMI module) have issues not powering off for power saving properly.
For the HDMI module, Framework has published a guide for those that wish to mod their older revision HDMI modules to get power saving to work like how it does on the new revision. As such, there is hope that for those skilled enough to do their own repairs that the worse off modules today may be able to be made better tomorrow rather than thrown away for a new revision.