I really think this should be reconsidered.
It causes a HUGE inconvenience (and confusion) for users who want to install FDroid in multiple profiles because you cannot install lower versions of apps you already have installed (downgrade protection) and this is true even across profiles in modern Android. So it isn’t possible to install and then update if you already have a later version on another profile. Since there is no transparency on the website regarding the app version, it could be very easily be seen as some other issue to those who are unaware.
Examples of issues - Cannot install F-Droid - Invalid package - using profiles - #26 by Sohika9539
I think this far outweighs the potential downside of issues that may or may not occur. Even if they did, you could argue that this would improve stability as these niche bugs could be reported then fixed. If it really wasn’t reliable, I would say it shouldn’t have been in stable.
Yes, it is possible to download an .apk of the newest version, but you could say that about downloading an older version too. Has it been considered to host both that version and the latest on the website?