I think the main problem here is the assumption that infiltration must always be the same as not being seen, and this is just not the case.
The main penalty for being a "sneaky" troll is that you get a lower agility score.
Yeah, sure, he's going to stand out when trying to infiltrate into a Humanis Policlub building and should get modifiers for "not fitting in"; but the reverse could be said for a human or an elf trying to infiltrate somewhere in the Ork Underground or anyone non-native-american trying to infiltrate into a Sioux bar. Who stands out and how much they stand out largely depends on the situation.
And a large part of infiltration, even when trying to sneak around an enemy compound, isn't about being invisible, it's about timing: waiting for that exact moment that the guard looks to his right or sneezes and then dash across that open space between those buildings. Here trolls even have an advantage: they can run a lot faster. They'll have an easier time getting over walls too, if walls/fences are built with human size in mind (which is usually the case), a troll might find them to be much less of an obstacle.
Half of the stealth group depends on Intuition instead of Agility too! Again, knowing where and when to move and when not to, where to stand, what to look at, etc.
A troll is always obvious? I can imagine half the bodyguards in the world being trolls; and bodyguard are invisible to most high-class people. Not because they can't be seen but because they just aren't important enough to be noticed. Put him in a tuxido instead of military armor and have him stand next to someone wealthy-looking and noone would think twice about him.
Heck, even when noticed somewhere he doesn't belong, who's to say Joe-Wageslaves first thought wouldn't be "A troll, trying to infiltrate? Yeah, right, Joe. Even they aren't stupid enough to think of pulling that off! Yeah... He probably belongs here, maybe he's the guy they hired to deal with the devil rats."