I'd probably try and trade your 6600K for an i5 7600 or 7500 instead. The iGPU on 7th gen and up can be used for transcode and will be a hell of a lot cheaper than a 3050 that is very overkill for just transcoding. It's good enough to handle 1-2 4K streams, and the single thread performance should be about the same, still being enough.
Everything you're getting makes sense and should do just fine. Plex isn't as difficult as you probably think it is, and if you still want to have a dedicated card for encoding, something like a Quadro P2000 should offer similar performance for a lot cheaper used.
I might also look for used server chassis for the case instead, something like a 24 bay Supermicro case would work great as long as you get a proper HBA. If you an find one for cheap, it would let you have a lot more 3.5" drives for the size. Just make sure to replace the fans with something a little less blowie matron.