Did you use the DVD image? If you want a self-contained install, then the DVD ISO is a must. You need an 8GB or larger flash drive. The minimal and boot ISO are for use with things like Packer where you just need to run the installer and get the rest of the install over the network. Having said that it's been ages since we've used physical media.
I don't understand why you say Gnome can't run scripts to start apps. We do it all the time, usually to customise the app environment before invoking the vendor script. We're more into development tools but large complex scientific packages like MATLAB work fine once you work around dependency issues. e.g., the 2021a Linux installer shipped with an openssl library that was the same version as the system library but depended on another library that wasn't available in the exact minor version required, moving it out of the way let the installer run. MATLAB 2019a needed different command line arguments to run on machines with older Intel integrated graphics. Both had runtime dependencies that were not documented. This is common for commercial software which supports only specific Linux distributions, specific versions, and specific hardware, and one is not using same. For custom software like this we repackage as RPM so we don't have to repeat the same work for each install. Gnome can be customised. When we moved to Fedora we used "gnome-classic-session" to bring back some EL6/EL7 features like the app bar at the bottom. We now use the same Puppet config on EL8. We were using Fedora before EL8 and were trying to emulate the former. I don't think I've seen what the EL8 UI looks like un-customised as all our workstation settings get laid down by kickstart and puppet. It was a lot of work to set up but that only needs to be done once. Now we can have a machine running with whatever setup we need in a very short time. If our user facing servers have a software issue, we find it easier to wipe and re-install than trying to fix them. We customise storage in the kickstart, so we only replace the boot volume. We use puppet to configure mounting other filesystems. We're a small department. A couple hundred clients, a couple dozen servers. Mostly it's just me doing "Linux" with occasional help from others. We invested huge amounts of time and effort in kickstart, configuration management, and software packaging. The result is that we don't see the problems you describe. All the software was free, which is amazing. It wasn't without cost though. The University of St Andrews is a charity registered in Scotland, No: SC013532
