Hey Doug,
Unfortunately, to be insured by schluters warranty you would have to use their caulk.
if your not worried about that, then yes you can definitely use another polyurethane sealant and be fine.
Sika flex is fairly reasonable at the big box stores
https://www.homedepot.com/p/Sikaflex-10-1-fl-oz-White-Construction-Sealant-90618/202529347
Silicon would be probably be fine if its not exposed to where the tile will be installed. Thinset will not bond to silicon, but will to most polyurethane sealant
