I feel you about the stabilizing pins and about Massdrop as a company - I prefer not to do business with them either, personally. (Still - nowhere else to get Halos!) That said, I think Brian P. has a great build going on there, and the Alt really is a solid platform. (Quick note - you don’t have to remove all the switches or take apart the case like Brian did to change the stabs. All you have to do is remove the switch between the stab so you can get the wire past it and you’re good to go.)
While stabilizing pins are optimal both for alignment and not having to butcher your switches, I will say the CTRL I have doesn’t suffer from any alignment or mounting wiggle - the switches I just popped into it are more straight than the ones I soldered-in to my Durgod Hades. 
A note about Zilents in particular - it seems the community generally considers them to be the de-facto best silent tactile (which isn’t unreasonable given Zeal’s proven quality) - but I have to point out an issue present in all the samples I ordered; out-of-spec resting position. Scroll down to the two bottom photos in this post and you’ll see what I’m talking about.
I don’t know if all Zilents have this or just the ones in my bag of samples - but I found this issue on almost every Gateron-manufactured silent switch in my collection. The main reason I mention it is that I believe it is an un-intentional result of how the top dampener is made, and it affects the travel and more importantly the feel of the switch. Even some of the linears feel tactile because of a “bump” created by the switch stem resting above its intended starting position, and sort of nestling-down into place before beginning normal travel.
No other switches I’ve seen (so far) besides other Gateron-manufactured silents (like Aliaz) have this issue - but not all Gateron silents appear to have it in equal severity; both the regular silent blacks and silent Inks I have do seem to rest a little high, but neither so much that the intended feel of the switch is changed.