After nearly three hours trying to track down why my very simple pants won't spawn as starting equipment while the other items attached to the same skill will, I have come to the conclusion that you can't actually have a character start with pants. It seems to be a hardcoded limitation, but I can't imagine why it would be intentional. It doesn't crash or anything, it's just the pants don't show up in your inventory, on your belt, or on your paper doll. I've tested it by just having my mod's skill call for pants from the main game (Cutoffs, in particular), which still don't load. Other items I've made and other non-pants armours called from the main game work fine in the same line of code just by using their names instead of the name of a pants item in the line of code I'm using.
Tested further with 1.0.9. The bug still exists, but it's more subtle than I'd realized. If you start with pants, they don't appear on your inventory or pants slot, but you still get them. They're invisible, and have no tool tip, and you can't take them off... but their stat boosts apply to your character until you try putting on some other pants. Then the invisible pants go away, never to return. Not sure if that's what was happening before or not, because the pants I'd been using the first time only gave a point or two of minor secondary buffs. To test it, I told it to spawn rubber pants with a particular skill. It didn't give me the pants but it did give me 2 points of each of the 3 correct resistances. I then found some adventurer pants a few rooms later and put them on. The resistances went away, without any item appearing. This may or may not be related to the "I ate a belt" bug someone was reporting in the bugs forum last week.
Invisible PANTS, not belts. (Though honestly, invisible pants are even more amusing.) I only mentioned the belts because there was a random bug report during 1.0.8 where someone went to change belts and the old belt just vanished... this was similar, except the item in question was invisible before it vanished. I too immediately thought "how do I use these stealth pants in my mod?" Then I realized the player will probably never notice since there's no way to see the pants and they have no tooltip. But I suppose you could make a nudist skill tree that gives big bonuses via invisible starting pants, which are then lost forever if you ever put other pants on for even a moment. Hmm...
Maybe I'll make them give neg stats and elude to this in the skill description. Something like: You're cold and embarrassed and should probably put some pants on. Then make them give neg Hyperborean and Existential resist XD
If you read the complete thread, you'll see that what your proposing is indeed basically what I eventually concluded. The pants spawn and apply their bonuses, but you can't see them and can't click on them or remove them. The only way to get rid of them is to put on another pair of pants, which then makes them just vanish forever. Similar problems sometimes happen with other bits of starting gear, but it's complicated by the fact that the game also sometimes doesn't spawn exactly the equipment you'd expect to get from a particular set of skills. For example, if you take the shield bearer skill (with no mods installed) you will sometimes randomly not get a wood shield to start. Which means it's sometimes hard to be certain if the missing item is genuinely missing or just invisible, especially if the item's buffs are subtle (such as a point or two of some fairly common secondary stat).
Yeah, I was just wondering if they actually vanish or are just moved to your backpack / on the floor (invisibly).
The testing I have done has not been able to distinguish between the two. I'm not sure of the true nature of what's going on, but in terms of in-game functionality, they are gone. I know of no way to make them reappear.