"If you are a TRS on .ca but not on .com (due to tracking BS) and you list on both .ca and .com, do you only get the TRS discount on what is listed on .ca and not get the discount on .com listings or do you get the discount for all listings."
Canadian sellers qualified for Global TRS status do get the 20% FVF rebate on eBay.ca and eBay.com listings.
"Wonder if Ebay will change that in the future?"
Based on recent history, yes eBay will change that in the future. Which way? Nobody knows.