By marking the settings in cloudflare > speed> auto minify as seen here https://share-inspiration.d.pr/scrlZT
will this interfere with similar settings in the Advanced area of Rapidweaver (as seen here https://share-inspiration.d.pr/icT22q) ?
Could this cause issues?
It could definitely cause some issues. Although CF really improved that feature this year to reduce conflict.
thanks for the input - makes sense. 
which leads to the next question:
Which is preferred? To leave it to Rapidweaver or Cloudflare?
I personally have it disabled on Cloudflare right now. Its been on my list to test it out again though.