I've asked around and most peoples' experience is that punch through does not go through allies. In most cases otherwise, there's something else going on in the confusion of a fight. Lag, projectile ricochet, the killing shot was actually from your sentinel, etc. I'm putting the sentence back into the Punch Through article, but if you're adamant that you can reliably shoot through allies, then we could record a proper testing of it to see if you're right.
The wiki states so for pistol / seeker mod.
That's usually the problem. When the wiki self-references, it can add to confusion. The fact that it's written as a tip on the Seeker (Mod) page is by no means affirmation that Punch Through actually does go through allies.
Well, for starters, when you say not going through allies, what are you referring to? Invasion allies? Other Tenno? Companions? I'm pretty sure I shot through my Kubrow who'd run up and hit an enemy, but I haven't extensively tested all of what "allies" could mean.
I've put it to some testing, and while I wasn't able to shoot through Tenno, I was able to shoot through a Kubrow standing still, with no allies about. Multiple times. (Getting the Kubrow to stand still in my way long enough wasn't easy). As to Invasion allies, it seemed to be the case when I kept trying to replicate it, but since the allies and enemies are shooting at each other, I'm not completely 100% certain on that one. Regardless, I stand by my decision that broadly stating you "cannot shoot through allies" isn't accurate.