I personally fit Trek into Who by reasoning that Trek takes place in one of the other Universes besides the one where Prime Who takes place. Both shows have purported that other universes exist where events unfold differently. The unifying thread is that I always interpreted the Galifreyans as existing in all universes at the same time, therefore "total masters of time and space" etc etc. Where we can really build a bridge is if the Time War loosens the Time Lord's previously demonstrated tight grip on "lesser species" interfering with time. In other words, The Time War is what allows The Sphere Builders and Future Guy their opportunity to attempt what they attempted, in the Federation Universe. I always felt that Daniels worked for a strikingly similar outfit to Captain Jack's original employers. Someone out there with better writing talent than me could probably turn this into a pretty good story somehow.