The levels for Hotoke Garan are 50. Nicholai is at 33. The endgame levels are 55, so 50 makes sense for me for Hotoke Garan. The damage average of 340 is endgame level (358) and does not take into account Jutendouji, Dark Seraphim, Great Question, Ultimate Weapons, etc. (and those alone drop the average lot), due to them...uh...not being available yet. I know Fenrir personally did take a strong set-up into the averages for damage for the bosses. I wouldn't consider the notes for Hotoke Garan underleveled (in which case, if you do, then that's odd, as most people view 55 as too high for endgame, so....honestly, I'd also call 19 at Edna a little low, and the SH3 notes I'd call lower in general, but I digress), and there is some consideration for higher damages in there. Now, combos are not included, as far as I know, but those should cancel out for both bosses (I know I killed Edna in a single combo, so combos hurt both their durability about equally - granted, in terms of set-ups, yes, Hotoke Garan has more to be held against him, and it does depend on when you do.
Edna does have to face some damage boosters - I forget which one, but you can get something crazy by that time. Granted, not as much as Hotoke Garan. Damage vs. Edna...I'll go pull my old save, but I'm fairly certain average damage is 100-150 or so, as noted previously.