Indeed, your question was all about 16-bit uncompressed output and refers repeatedly to making only two formats "MP4 + MOV". Parallel transcoding to a large number of variants is a totally different question (not sure how you can get to "50+" unless there's something seriously weird about your workflow).
Professional studios do not use Adobe software for mass transcoding. They use enterprise systems (hardware- and software-based) such as Telestream Vantage (used to be Episodes) or Elemental (now part of AWS). With those systems all the rendering happens on distributed hardware or arrays of AWS instances. Very effective, very fast, very expensive.
The logic I described still stands though. Assuming there are no resolution-dependent content changes, you always render a single master file from your NLE, and hand it off to the transcoder. What the master format is will depend on the transcodes and software being used; a broadcast or theatrical release that transcodes in-house and includes DPX in the delivery pack will often use DPX/EXR right through, but then you're looking at up to 2GB per second for storage. Pretty much everyone else will use ProRes, DNx or Cineform in some flavor; there are quirks in the transcode math used by each pipeline that favor one or another (e.g. avoiding YUV<>RGB) but that's not an Adobe-specific matter. You talk to Telestream/etc. to find out what they suggest, then run tests and look at the SSIM/PSNR values in Switch or Netflix's VMAF.
You cannot "streamline" out the need for your NLE to render something, and for that to be subsequently converted. You can speed up After Effects rendering of image sequences by installing CC on several computers and running the aerender.exe app, but it's not worthwhile unless you have a bunch of idle workstations lying around the office. You can remove the need to click buttons in Media Encoder and sit waiting for the universe to end by doing what everyone else does - hand Telestream all your money. Creative Cloud is not an enterprise-level transcoder.
And it is perfectly possible for Media Encoder to produce more than one output from a Watch Folder item. Just click the "add output" button on the tab header after you have set your watch folder location - but it's pointless trying to render a mountain of different outputs on a single computer, if nothing else because Media Encoder is incredibly non-optimized. Most of your cores will be asleep.