To be honest, if you're having problems with early deeper stacked play it might be that you are pushing a bit too hard with top pair/overpair type hands (as indicated by the "early hands are the most damaging" comment).
Deep stacked play is about implied odds, which favors the suited connectors/small pairs hands, rather than the big pairs/top pair top kicker type hands. Obviously the donks will be playing dominated hands like KT and will usually be paying off your AK when a king flops, but those times they outflop you can be costly if you aren't using pot control sometimes with your one pair hands.
+1 to "entering late is a bad idea". It does seem like it might come down to how well you play a deep stack though. If you're -EV above 50bb it might work out to register late. However, I think a superior maneuver would be to learn how to play deep stacks.
I'm pretty comfortable at the early stages of a tournament. I know for sure that I'm almost never going to bust out on those stages. That's part of solid play in those spots, rarely going broke.
Imagine a good player registering on time vs. a good player registering late over 100 tournaments. There are a few broad categories the 1st player will be in by the time the 2nd player registers.
1) Stack is essentially average, perhaps slightly below. Solid early stage play, just didn't see any
hands or get good spots.
2) Out. Got into a confrontation (likely with a spew-y fish) and got unlucky. In almost all of these spots the good player got their chips in with +EV.
3) Big stack. Those same confrontations from #2 worked out in favor of the good player and now they have a nice stack.
#1 will happen most of the time, say 50-60% of the time. Of the remaining 40 tournaments the good player will have a big stack far more often than they will be eliminated. Let's just give a standard line of 2:1 favorite as the average
equity our 1st Hero had in their all-in spots. So 27:13, 27 times the 1st hero will be double-up or better, 13 times they'll be out.
Scenario 1 is +EV for the player that registered on time. Stack sizes being essentially equal, the 1st player had the time to develop reads and build an image (probably a tight one that will make stealing easier).
Obviously scenario 2 is +EV for the late registering player and scenario 3 is +EV for the standard time player. Overall the guy who registers on time will be
way +EV over the one who registers late.
Edit: Regarding Phil Helmuth, he shows up late for major events. Levels take over an hour in those things and players are starting with 200bb stacks or something. Helmuth is walking in with essentially the starting stack and 1st level blinds, so it's very different than an online late-reg.