The aspect of weather a season normalizes "well" depends on what you're comparing it to. For example, a pitcher from 1968 doesn't "normalize well" because his real life stats will look much better than his normalized or # stats. When a 1968 pitcher has a 1.00 real life WHIP and a 1.10 WHIP#, people will say he "doesn't normalize well" based on the fact that his normalized stats will be worse than his real life stats. That's just semantics of some of the users around here.
You are correct that if you look at the # stats, then a 2.50 ERC# pitcher from 1968 should be the same as a 2.50 ERC# pitcher from 1935. But the 1935 pitcher "normalizes well" or normalizes better than his real life stats and vice versa for the 1968 pitcher.
Where this really matters is in the salary though, because salaries vary for players based on the normalized stats. Here's a random example:
1963 Art Fowler - 90 IP 1.00 RL WHIP 1.03 WHIP# (normalizes worse than real life) 2.04 ERC# $2.82 million.
1991 John Hayban - 90 IP 1.03 RL WHIP 1.03 WHIP# (normalizes about the same) 2.06 ERC# $3.18 million.
So one "Normalizes poorly" and the other "normalizes well (or at least OK), but the price difference is substantial (and granted, Hayban gives up fewer HRs, so I imagine that might make up for the difference). So while both have similar numbers, Fowler is cheaper, but Hayban's normalized stats are closer to his real life numbers and will be perceived as "normalizing better" than Fowler.
Also, the sim uses the actual OAV#, BB#, K# and HR# stats in the log5 formula for ABs, so just looking at ERC# will not tell you the whole story. In the example above, Fowler has a RL .219 OAV and a .227 OAV# (again, "normalizes poorly") while Hayban has a .225 RL OAV and a .227 OAV# ("normalized less poorly"). While both wind up .227 OAV#, again, there is a large salary discrepancy due to how their stats normalize. Since the league average for each player is used in the AB (both the pitcher and the hitter), Fowler is more likely to "help the hitter" (as his OAV normalizes poorly) than Hayban (whose OAV normalizes closer to his real life number).