Getting back to the OP, I don’t see super-heavies changing warfare that much. They require too many assets to build, too much in the way of logistics to transport and keep in fighting shape, and they don’t do much beyond taking a long time to die. I would expect them to show up as permanent defensive units of planets with a robust military infrastructure. So, capitals and centers of industry. That way you can ignore transport, and mobility isn’t much of a need, but you can still be less predictable than a fixed gun emplacement as a defense.
While using them to defend fixed points
eases the logistics by orders of magnitude, super-heavies are still limited by their strategic speed. A super heavy can have a major impact, but unless it's packing arty, it's not a big threat to anything more than a mapsheet or so away. Yes, the same is true of any other unit using mech-scale weapons, but it's a lot easier to reposition smaller units, both tactically and strategically.
Look at Devils Tower as shown on JHS:Terra, pg 202(205 of the PDF) [rant] If Catalyst wants to do PDFs, then they should make the page numbers in the index and TOC match the page of the PDF in all readers, not just the blessed Adobe[/rant]. The Devils Tower Castle Brian is about 2 km^2 in a roughly 2km x 1km layout. Even if there is a straight and flat tunnel, it would take a super heavy 4 minutes, or 24 turns to get from one end of the complex to the other. There are heavy mechs that can do that in a third the time.
Depending on the granularity of your table top, that makes for some interesting counters to super-heavies that don't boil down to "hit it harder." It becomes a game of faking out the defender with a feint toward one target, then repositioning, either via relatively fast ground units, or a short hop via jump ship to the other side of the city/base/complex.
I imagine this is something that would be handled via dice/negotiation before the actual battle starts, otherwise it would be rather tedious.
True, the same limitation applies to super heavy vehicles, and even some regular vehicles, Burke and Mars, I'm looking at you. And to be fair, an Atlas or Dire Wolf might be
almost twice as fast, but to be honest, 3/5 is still painfully slow.