Warming Up with the thing you are trying to Warm up for.

This is something I've been meaning to ask, as no matter how I warm up and I have tried long warm ups ie 15-20 mins deconstructing the exercise and then conversely  just going straight into it and have found that there are some exercises and iM's  like cossack squats and the  iM that don't really click in till the 2nd set, while the MN/PE1>im ie SLW doesn't really get going till about the third set. 

so I guess I am wondering whether they should be considered as the warm up or count them as working sets and just let my ROM catch up over time ?

Yes, inquiring minds want to know if warming up by doing jefferson curls, dislocates and twisting squats is cheating to achieve full ROM in the first work set.  

I wouldn't say that it's cheating at all for training but the assorted mods/coaches in the linked thread below reached a general consensus on whether this strategy could be used to test for mastery;

 

https://www.gymnasticbodies.com/forum/topic/15302-mastery-only-after-long-stretching-session-mnpe2/?hl=%2Bmastery+%2Bcold#entry149101

Great.   My tombstone is going to read:

 

Here doth lie the nutter who could not master twisting squats.

That seems a bit strict, ie to be able to call up full ROM and flexibility on demand. Most athletes of all abilities should and do warm up prior to any activity.

^^^Yes true, but high level athletes warming up is more about increasing the core temperature of the muscles, synovial fluid in the joints, and general injury prevention. A baseball pitcher for instance would be capable of throwing his fastest pitch right out of the gate, it just wouldn't be a great idea to do that very often.

Also, it could be argued that perhaps maximal performance requires a general and specific warm-up, but I think the idea with being able to claim "mastery" is that these skills become sub maximal for us, thus not requiring the same degree of warming-up and us being able to demonstrate them at the drop of a hat.

So does that mean I shouldn't count the sets that full ROM is not being achieved or at least not smoothly ?

If you're playing by the rules, you shouldn't count them (they're just missed reps) but at some point you have to monitor progress somehow - and that probably means er, well, counting something.

Count your best reps. Check they're getting better qualitatively (video) and quantitatively (how many). Wash, rinse, repeat.

When I was torturing myself on straddle ups I used to do a set. Watch it back, see how high the best reps were and then work to better that number in the next set. It worked eventually and I got to a point where it was worth starting from Wk 1 again at full ROM. Of course I had good days and pitiful days but then I still do!

Coaches templates state what is required for Mastery.  Warm up any way you want, but you must still perform the requisite (sets x reps) for Mastery.  Adaptation should continue if serious effort is being applied so that one gets more proficient at the beginning of the exercise as well.  I wouldn't worry about a few reps being off a little at the beginning as they can be made up at the end of the set.

As long as you do the mastery reps correctly I don't think it matters how you warmup.

 

In my opinion there are some exercises are best warmed up with themselves, like shoulder dislocates, which I usually I need to do a couple of reps at a much larger width than what is my current best.