The Apps tab will
Not display anything incompatible unless changed in it's settings for new installations
Not display anything deprecated unless changed in it's settings for new installations
For a reinstallation of an app which you've previously had installed which is now either deprecated or listed as being incompatible it will allow a reinstall, but is clearly identified as being deprecated or blacklisted.
Will NEVER allow you to install anything that is outright blacklisted for one reason or another
Opt-in: Periodically scan your system and alert you to the presence of:
1. Known malware and security vulnerabilities within applications
2. Critical security vulnerabilities within Unraid OS
3. Any installed applications which may seriously hinder the operation of your server
In theory, there really should be no cases of "incompatible" docker apps with anyone's system due to the nature of the system. The whole system though is moderated and when it appears that a particular app is causing issues for many users, it gets investigated and any applicable action deemed necessary is taken. In terms of your problems with nVidia and Plex, any of the available apps should work just fine, assuming the plugin is up to date and the hardware doesn't itself have issues and is supported by the driver version (I personally use @binhex and bounce back and forth depending upon my priorities on reallocating hardware resources between various computers use either nVidia or Intel transcoding). Plex Inc though is one of those software companies that tend on their constant updates to break something else, and "good" releases are rather rare compared to the number of updates they issue. Part of my reasoning for using binhex, as while its updated regularly, it's not utilizing the bleeding edge of Plex (which they always label as "stable". Many others here will disagree and say the opposite and that Hotio or LSIO is the way to go. To me, its the same as AMD vs Intel or GM vs Ford)
Additionally, Fix Common Problems will (amongst many other tests) alert you if you have installed anything deprecated, blacklisted, or incompatible (and in the case of plugins - unknown) installed
RC2+ fixes an issue where some users experience hard crashes of the OS when containers / VMs run on their own IP addresses. It offers the option of ipvlan as the driver instead of simply macvlan. The actual differences between them are above my paygrade...