I think you should treat secret levels as extensions of the regular levels you get to them from. You don't really get tallied for bonuses after destroying a secret level, so...
Damn, I still wish D2 gave the liberty to make D1-like secret levels too.
Yeah, I wish D2 secret levels were more like D1. Also, since demos dont track bonuses apparently, I dont think that's going to make much of a difference.
And if I were to incorporate them as extensions of the levels they are attached to, would that mean you'd want me to run level 3 + SL 1, Level 4 + SL1, Level 5 + SL2, Level 8 + SL 2, Level 12 + SL3, Level 14 + SL4, Level 17 + SL 5, Level 20 + SL 5, Level 21 + SL 6, and Level 24 + SL 6?
Seems kind of odd.
I'm thinking it's probably best to treat them as separate levels, just entered differently. The DOS mechanics for recording secret levels seem to imply that that's the only way to go about it anyway. Demo recording automatically ends when exiting a secret level.
Further, Rebirth currently has a bug where demos that transition from a regular level to a secret level terminate upon entry and drop the viewer back to the title screen. I found this out the other day when I tinkered around with SL4 and ran it under my Insane-Max rules. Got a time of about 1:40, but to view the demo I had to load it on Dosbox.
I have reported that glitch on the Rebirth forums. I've also mentioned that I'd like it if demos could be set up to continue recording when transitioning from a secret level to a normal level. I might also request a way for Rebirth demos to track bonuses and other things.
So I'm probably going to treat D2 secrets like I do D1 secrets: clear a path to the levels entrance and then use the exit with my ship in a cold-start configuration. What that means in D1 is clearing a path to the reactor, suiciding, blow the reactor up using only level one lasers, and then take the exit with no powerups. Then save upon materializing in the secret level. In D2 it will mean clearing a path to the teleporter, suiciding, and arriving back at the teleporter with no powerups + exactly 100 shields + exactly 100 energy + 3 concs, and making a save game right in front of the actual teleporter.
All six of the D2 secret levels are doable under my proposed rules for Insane-Max. Secret levels 1, 2, 3, 5, and 6 all have enemies to kill, all six have one ups and possibly a full map powerup to collect, and SL 4 has hostages to rescue. For secret level 6 I would be counting each mini-reactor as an enemy. For secret level 3 I would be killing the thief only once and then ignoring the respawns under the "enemies the level starts with" rule.
And for secret level 4, I would need to collect all 7 1-ups, the full map, and the hostages before exiting the level. And to do that with the fastest route, it means using the short-cut near the start of the level that skips to near the end, and then opening the door that leads to the 5 one-ups using a guided missile instead of shooting the well-hidden trigger that shows up around mid-level. And yes, you can open locked grate-type doors with guided missiles. I do it all the time. In fact that's how I open the first door in secret level 4 most of the time when I play through D2, that way I can just take my time and grab all the stuff before I blow the place up. Just have to thread the guided dead center through one of the holes, as grate-doors offer no margin for error unlike regular grates. Not too hard.