A Hardware Compatibility List (HCL) is completely reasonable in my opinion for building your own machine and it's well known that Nvidia and Linux don't play nice. Recently built a new system and went with AMD for that reason. Considered Intel but they're a little new to GPUs and were a little too mid range for what I wanted.
Frankly it sounds more like you had issue with the Nvidia card than the rest of your components.
Also have to consider are you trying to use completely free open source software or are you okay with proprietary blobs and drivers.
For example Ubtuntu makes it easy for end user to activate those proprietary software blobs on installation.