The chokes are just to provide DCS signal isolation. If you don't use them, each Fastrack switch degrades the DCS signal a little. If you have a bunch of them, you can run into signal issues.
The MTH remote does NOT control TMCC switches, you'll need to talk directly to the TMCC/Legacy command base with a Lionel remote. You have to use the SWITCH function on the remote, MTH doesn't support that.