I was too young to remember clearly at the time, but I think I experienced the Vykhino railway-metro connection a few times in the early 2000s. I don’t seem to remember the original connection that’s said to have given the name to the “Vykhino effect” (wherein the suburban rail arrived at and the metro departed from the opposite sides of the platform, and you could cross it unimpeded, leading to the metro trains being completely full straight from the first stop—the “effect”) was still in operation then. I think the fence was already there on the platform and you had to use the disgusting, stinky, cramped tunnel? (That before the railway started fencing away everything in the name of better ticket controls.)
Yes, the Metro trains were chock full (think Tokyo), and you could only board a train if it skipped Vykhino if you needed to do so on some later station.
I don't think it is possible to be physically unable to enter the train in 2023 (unless football fans return from thei match). In 2003 it was expected.
I, too, dislike the new connections, and the lack thereof, but the speed with which the new lines sprung up is a marvel.