Dave,
I don't know if PF3 could do it but if the user a/c was contained in a bubble say of 150 meter radius. Could PF3 detect any ai encroaching anywhere into that bubble as it moves? So any ai finding itself within 150m in any direction of the user has to stop as the user passes by, or through an intersection. In addition you could compare the ground speed of the user against that of the ai and if the user was ai+50% then "[callsign] Hold your position." Thus reversing the process and not stopping ai. Then once the ai has passed "[callsign] Continue taxi." It doesn't matter then at what angle the ai is to the user. Also if the ai is already stopped eg. waiting in a queue then you could omit that call.
So in effect there would only be three parameters for PF3 to check Is ai and/or user moving - plus "You're too close to me - Stop!" or "Oi you the rally driver - Stop!"
If PF3 can't then we have to go with what you have done.
Well PF3 does use a 'bubble' radius but only to the front and sides. The routine then calculates if anything moving within that radius will, within the next 60 seconds, either enter our assigned taxi route and/or cross it. CM is a totally separate process to PF3 so it cannot issue hold instructions. If you remember this was a point I made during the beta because I wanted to give CM every second I could at searching for possible conflicts. If it had to stop for say just 10 or 15 seconds to issue a 'Hold' and wait for a reply, another conflict could easily slip through the net.
CM was designed to be a transparent as possible, to just sit there and prevent any conflicts without you even knowing about it. If you notice any aircraft stopping prior to a possible conflict all the better and you might just assume it was the pilot using common sense rather than waiting for ATC to tell him/her they'd better stop before crashing into another aircraft
I always knew there would/could be a problem of CM stopping an aircraft at the furthest point away from you which was actually on your taxiway and so on reaching it you wouldn't have a way past it, without going on the grass

, which is way we have the 'stop CM/restart AI' feature, automated by your speed. So you see an aircraft that has stopped and as you slow down it continues with it's taxi. If you're careful with your speed you can simply follow that aircraft all the way to the holding point with no further stoppages but yes, if you go above your trigger speed it will stop again. That, I believe, is a small price to pay for a feature that works really well, even though I say it myself.
I think my throw away suggestion of maybe having another hotkey to toggle CM off/on will probably be the best thing to keep everyone happy.... so if you use the hotkey to turn CM off when following along behind another aircraft it would not begin working again till you hit the hotkey a second time.