A Pro Angler 16!! Wow! Didn't know Hobie released a new version...lol. Happy Holidays!
All kidding aside...congrats on the new PA whether it's the 12 or 14. To answer your question...as long as you have the support say around the front and rear scupper hole areas, you should be fine. That's an interesting approach and one that I have not seen mentioned, but it sure sounds usable. The canvas base would cover a reasonable support area on each end and would be no different that some cradles.
Welcome to the Pro Angler family! Looking at your "handle"...Merry Christmas from one Tar Heel to another.
2013 Pro Angler 14 - Dune
2015 Pro Angler 14 - Papaya (soon!!)