I have been confused until now why I was missing the 'third party' button, to mark for instance my MDM solution as satisfying the recommendation. I notice the option is on the first dashboard tab/mode.
accessing the recommendations via the 'score analyzer' yields neither 'ignore' or 'third party'
I have used the third party option and it has taken the score into account successfully. i'll now try on other 'third party' options.
Note, I'm not actually using a third party. I'm using ConfigMgr CB 1802 in hybrid mode (it is the MDM authority, but implements using InTune, I understand). Detection is not implemented in this mode though, if I'm right.