The product template has to be chosen in the admin. You can't upload a CSV file with products and say "use said template" because it doesn't have the permissions to create that template if it doesn't exist. I think you can imagine a scenario where where someone misspelled a few product templates in that column and then Shopify creates a bunch of product templates that don't need to exist. It would just cause more issues in the long run. Better safe than sorry.
Hey there. This has not changed, However I may have a solution for you.
What I do it my store is use Tags which can be done by CSV. I use like Template1, Template2, etc
Then when you go into your product section after upload you can do a search accordingly.
Then you can hit Select All, and Edit for the bulk editor. Once open, Click the first ones Template field, Hold Shift. Click the last one. Change the template on the first one and it will change on all of them. Hit Save. Move onto the next page if needed. You can have upto 250 items on each page showing.
If your tag has a space in it, you can search it with
Making the tags easy makes it easy to remove the tags after in the same Editor mode.