What you say sounds right. I grew about 30 TBH nucs this season, and only had 100% flat, parallel combs, so uneven combs were not an issue. I can visualize how uneven comb surfaces, especially wavy combs could present some challenges. Though with irregular combs, wouldn't even the 'steel rod' technique be difficult, the irregular combs would roll/smash bees even then.
I use top bars with straight wooden comb guides. I pre-start the combs for each TBH between brood combs in already established colonies, which themselves already have straight combs. Sometimes, if they begin building drone comb, where I don't want drone comb, I pull it off and let them start again, but usually they change to worker cells on their next try. It often only takes a day or two before they've built the beginnings of nice, straight combs. I then gently shake all the bees from the 'started' combs, put them together in their own box, then select an already established colony, move their queen to the new top bars, then shake all the workers over too. If there isn't a flow on I will push a parallel crack between a pair of top bars, 1/4" wide, then place an inverted quart feeder of 1:1 and a very small pollen sub patty, to cover this crack. If this causes the comb surfaces, adjacent to the crack to be drawn out too far I carefully cut them down a little to avoid bee smush, before pushing the back together. It sounds complicated, but has worked well, so far.