Skeletons don't Aggro from huge distances or use a horde mechanic. The problem is definitely not a lack of food, between zombies and silkworms. But try following the quest progression naturally. You can not do anything involved in one of the quests until that quest is unlocked. No furnace until you make a stone hammer, bone crook, bone dagger parts, and a full set of wood armour. It's... Well, pretty tricky or downright impossible. The time required and the dehydration per minute are just too much. :x Sure you can make more dirt to plant more saplings, but even with 20 of them in a compact 5x5 farm when I was playing on the old map, I was usually off sifting or crucible-melting and just chopped anything that would happen to grow. Without shears, there's no way that can be a reliable source of water via saplings into fluid transposer. You just need that bone meal, and thanks to Dinnerbone it takes way too much per tree now. :x
This is all going to be moot for anyone who makes a dark room, even a tiny one. And it sounds like ZA is coming back in the next version, anyways. I'm just musing about possibilities, order of quest progression, and survival techniques. There are always new tricks to learn. I'm curious what opinions are on the most efficient bone meal to compost yield. 16 bone meal for one dirt from rice, how does that compare to infested birch or infested oak?
If you have any other advice, I'll give it a try. Part of the fun of additional challenges is finding clever ways to overcome these hurdles without compromising 'the rules'.