I'm fine with all Guardian being a viable option oh, but the last thing you want is for the only viable option for Guardian gear is all Guardian. I would certainly be down for Guardian gear tending to work together synergistically, but I think the bonuses should be independent of other Guardian gear, in a similar vein to the guardian power distributor. I often use that module on ships that need a little more power, and are not particularly distributor hungry. In my ideal world, all Guardian modules would be like this; I only wish they would add a similar effect to the guardian power plant.It wouldn't be a terrible thing to have an all-guardian shielded build as an alternative to the shield-less cold-running meta. As for the odd hardpoint, I don't think it does force players to think differently: the poor placement basically gives two options: Multicrew or Gimbled Thermal Vent beam. Multicrew isn't much of an option for a solo-player and thermal vent is already the default (and the fighter already provides a Multicrew option).
If I were trying to push a Multicrew option, I'd let the ship break the 4 AX weapon limit, give extra small/medium hardpoints with terrible convergence and release turreted versions of the modified guardian weapons. Maybe something like three Larges with tight convergence (intended for the pilot), one medium with lousy convergence siting up and back on each wing/pylon with convergence comparable to an Imperial Cutter's wing mounts. Size the PD so that you'd need multicrew (extra pip) to make effective use of he medium hardpoints. Release a shield-less fighter with meta-alloy/guardian hull reinforcement (Fluff... basically no shields, much more armor, and immunity to corrosive). Armed with AX Missile and Flak.
I'd also be very careful of allowing players to break the 4X experimental limit. Much of the high-level thargoid content is balanced around very specific DPS totals. Adding even a single ax hardpoint could quickly take a fight from difficult to easy.
Lastly, I disagree with your assessment of the odd hardpoint; Yes, it would be difficult to four primary damage weapons, but given the other advantages of the ship, players may be incentivized to attempt to use it anyway. Alternatively, they might find a way to use a weapon with slower projectile speed, to maintain combined fire at a certain distance and orbital speed. I do that myself, using my Corvettes and different sizes of cannons.
This often doesn't work with current ships, but that tends to be because they are bilaterally symmetrical, which requires more of a rocking motion, which can become too complex to handle, especially given the other distractions of combat. A single offset hard point is something that we haven't really seen before; especially not with such a large amount of Firepower concentrated into it. Sure, it might not work, but at the very least, it would be a very different and intriguing ship, giving something for players to play with. And hey, even if it doesn't work out, what's the harm? You can always just design another, and then you've got another unique and interesting ship in the game. To me, that's a no lose scenario!