Yeah me too.
(Initially, I also had some trouble with different typings for client JS, server JS and shared JS)
If you mix and match TS with 'regular' JS files, you are in for some pain. It's best either to go all in or not at all. The reference system of TS is both good and bad in the form it is right now.
For instance, see -https://www.reddit.com/r/typescript/comments/315ae4/newbie_question_is_it_possible_to_slowly/. Quoted, "You can mixe your code, but be careful with the file ordering."
I tried TS on an old ~3k standalone JS file. I incrementally moved to TS (so a part of it was JS, part TS). That worked out fairly well.
IMO in the long run as more and more people jump on the TS bandwagon and these things come up, the TS team is going to make it more easier to use TS. Right now everything is configurable and that's a blessing and a curse. Opinionated TS would be nice for the general mass - something, which if Meteor offers, will set it quite apart.