I'm not sure if a restructuring is necessary.
For all we know, the mass effect -fields forming the beam could just as well be conducted by the tower's outer hull alone.
I'm more of based "reconstructing" because we know for a fact the Citadel changes to work with the Crucible once it docks. Even changing into more of a star shape. And as past images show, there was no choice platforms before the crucible docked.
...which makes you realize once again how thin the whole plot is with the Crucible. Even if it was originally designed by someone who was aware of the Citadel AI, such and such, how the hell did we build this entire thing and not know anything besides "It can release a large amount of energy" and not to mention those three arms it has which grabs the Citadel ring... I mean, how were they ever in doubt that the Citadel was the Catalyst, just judging by the size match on the blueprint?
Any way I see it ME3's entire plot just collapses under its own weight.
There's actually an easy answers for that one. Catalyst was never something anyone though was suppose to be "found". We knew there was a missing part called the Catalyst, but the assumption I think was to find out what was the missing part, and build it. Not find some giant object that the Reapers haven't destroyed during the Prothean cycle. Especially since that cycle failed to use it. The Citadel also being a suppose Reaper creation also would've thrown anyone off the sent. And even if someone did think of it, they'd look at the ring on the Citadel, how the Citadel could attach to it, see the same images we saw before the crucible docked, and go "Yeah, unless the Citadel has some hidden functions, and changes in some way we don't know about (which ended up happening), this thing could never work with it".
So yeah, there you go.
Now about the Catalyst and the Crucible, I'll update this on the main page later when I get the time, but one fact we do know is that the Crucible possibly was once a device that had nothing to do the Catalyst. It was created to work as it's own independent thing, that sadly never worked. The Prothean VI tells us things. Eventually, "something from another cycle" took those plans, and adapted it to work for the Citadel. Whether this is true or not, we're not sure. But the Prothean VI is believes it. If true, I believe it was the Leviathans or the Catalyst itself that might've added the "adaption" to it, since it creations solutions it wants instead of just taking out the Reapers.
Whoever made adaptions to the crucible are not the same as those who came with the original design. After all, we know the Protheans. And we know they made their own changes. The Protheans are not "someone who we don't know". So it's possible whoever made the adaptions to the crucible to work with the citadel is someone we may know. But that is speculation.