The request for external midi control has been asked before. Linked is another thread where Squarp responds that it’s not currently in the near future plans. They are asking for something more broad, but transport control would be covered under that umbrella and has been mentioned specifically.
They did add a lot more options for different things you can control via TRS footswitch in v2.0. If you need a short term solution, I’d figure out if there’s a way to use midi to automate a normal passive TRS footswitch signal into the Switch input.