gavra, the difference I can see is that if they hold R”T l’halacha and take the Gra as an added chumra, m’ikur hadin they’re only bound to their shitta (i.e. the R”T). As a practical matter they’ll probably always use the Gra as a chumra. But bshas hadchak they might rely on the R”T, without using the Gra’s zman l’chumra, in case of a bona fide emergency as their adherence to the Gra’s zman was only mekabel as a chumra and not as psak halacha. BTW, this same point would apply in reverse for those who accept the Gra l’halacha and take on the R”T l’chumra.
Does anyone consider those who [start and] end Shabbos early to be a Mechallel Shabbos because he doesn’t wait for the R”T’s zman for Shabbos to end? In that case we have lots of non-Shomer Shabbos folks davening in many non-chasidic shuls. There’s another queston for mw13: Are those ending Shabbos before the R”T zman doing the same as those starting Shabbos after the Gra’s zman.
As far those “(but not all)” who don’t even take the Gra l’chumra, and stick only to R”T kipshuta, I’m not sure how’d they’d answer your milah question. But if they rigidly followed the R”T on the zmanim, they’d be halachicly consistent. I think the R”T himself, and his kehila, would have the bris on Shabbos.
R”T is not chopped liver. And at the end of the day, members of kehilos who strictly follow R”T kipshuta, and have a mesora of following the halacha as such going back to their kehilos in Europe, have solid halachic ground to do so. Even if the M”B disagrees.