No, i think the suggestion is in cases where perhaps two factions are "balanced" but one requires more micro (think US crew repairs to make up for the fragility of their tanks, or having to click on the ambulance heal instead of a passive heal). If 40 APM will be able to handle one faction and 50 or 60 will make handle the other, then for someone with 70-80 apm all the factions are an L2P issue.
For someone with 30 apm vs someone else with 30 apm, those factions are imbalanced even assuming perfect game knowledge on both sides. One will be able to get more out of their faction than the other one would out of his/hers. This gets exacerbated by the asymmetrical-over-time balance (which you were complaining about). More mistakes on both sides also means the games will last longer as each side makes mistakes, but longer games in COH2 are much worse for Allies than they were in COH1. (Not least because you get to "late game" faster but have the same VP system.)
So "balance" does mean something different at different levels of skill, not just different levels of game knowledge. COH1 (in its later stages) didn't have this. At almost every stage of the game US vs Wehr was a L2P issue, not one of assymetric faction design.
Those are subtle mechanics that should be there (at least in my opinion) to distinguish good players from great players, there were actually a lot of those in vCoH, the first example that comes to mind is the motorcycle micro that you needed to make the MG Bike combo work, you needed a lot of control for that kinda like the one you need to do that fast repair on the tanks. That, however, does not mean that if you balanced the game from the top players that it would mean you had to micro more to make a faction work, those are little things envolving the outcome of the game. Assuming the factions are well balanced AND designed, design being key, means that each factions has its little "secrets" and perks that only top players will make most use of by being faster but that does not mean that the faction as a whole will be unplayable for players with less micro. Again ill refer back to US vs WM on vCoH since I believe it was done to near perfection, US was a faction that needed most micro to make it work at a top level that doesnt mean that at a lower level of play the faction was better or worse because you still had the things you needed and those easier to use units or whatever you might call them, just that as a player gets more efficient playing a faction they can diverse from that type of play and make more use or better use of riflemen for example (big part of US gameplay both in Coh1 and Coh2, that requires a lot of micro to perform well).
EDIT: I also would like do distinguish "normal micro" from "smart micro" , which is why I believe game knowledge is heavily into how efficient you can do things in coh2, if I know more or less when a unit is going to throw a grenade, I know the timing to look back at the unit when I need to to ensure that it didnt get grenaded, that is in my opinion smart micro, while I guess people must think that a player is so fast that is always watching if the guy is going to throw the grenade. There are A LOT of these examples, im able to do so much in a game so quickly because I have the game knowledge to back up my micro so I dont do unnecessary clicks or keep my focus on the unit that is right while not losing the others to small little details.