I do not understand everything exactly what you want to do with maschine in PT :)
But I can say the following.
I use Maschine a lot (stand alone) and I love it.
And Pro Tools is my favorite DAW since 20 Years.
And now the Problems:
You can use Maschine in a DAW/PT as Plug In in 2 different ways.
1. using it as sound device. (without the maschine internal patterns/sequencer)
you can trigger any sound with a midi track from PT. In this case you record Midi in the DAW/PT. This works good and the ADC also works fine.
BUT (!) only with 44,1kHz. in higher sample rates (88,2 / 96) it is unusable, because you get double notes. this is a known maschine AAX bug.
there are videos who describes how to route midi from PT to the sounds of maschine. you don't have open more than 1 instance.
you can adress different midi channels and route machine sounds and groups to separate pro tools aux
2. using it in "maschine mode" (with its internal patterns)
in this case the sequencer of maschine plays in sync with the DAW.
here you have all the performance and recording features as in the stand alone version. only the start/stop is controlled by PT.
BUT here comes the second maschine AAX BUG. in this this mode the patterns of machine are NOT delay compensated with the ADC. so it is complete unusable in Pro Tools (it worked in PT 10) since PT 11 NI has not get this under control.
you can disable the ADC for the maschine track (this is a idea from NI support). in this case the patterns are in sync. but this is not a recommended workflow, because in this case you can only playback the patterns and you can not play new patterns with the pads, because the PADs are complete delayed.
the only solution is to use machine in maschine mode (with its internal patterns) with vienna instruments (as VST) is the only way to get the maschine patterns in sync and in this case you can use it without latency problems and full features of the maschine internal sequencer (patterns)
hope you understand what I mean :)
thats what it is.