I have a similar use case to yours which uses Tone.js to download a Midi file into a midi object, then alter the midi object (according to user settings) and then be able to play the changed midi, with the ability to change volume and tempo. This post was very helpful to achieve that.

Using Part does indeed make it easier to manipulate Tone.Transport. In my project I load a sample Midi file, there are 2 midi channels (channel 1 and the rhythm channel 9). The logical thing would be to have 2 parts, each having their own instrument. Is this the approach that you (would) take?

I also wanted to mention another interesting example I found that uses Tone.Part and Tone.Pattern: guitarland music theory