I had great problems checking in at a TAP business desk in LIS earlier this year, with an FTL card. It is true that the check-in agent in question seemed more interested in re-doing her fingernails than anything else (I was the only client, so wan't depriving anyone of anything), but I had to quote m&m rules (made up on the spot) to get service.
It seems to me that the conditions in M&M brochure are not entirely clear (I reread them on getting back home). It certainly isn't clear whether they apply to only LH (and presumably to partners who do LH check-in such as SK in Scandanavia, LX in Switzerland, etc.) or to the whole of *.