Three foot could be a little small but I see that can't be helped. Plenty of run time will be good for them, as you suggest.
I have a friend who keeps their pair of boars in a three foot cage, and they get to run around the kitchen for several hours each day, and seem perfectly content. I've seen small cages and run-time work for other people and their piggies too
However some get stressed in a small enclosure..... personality can play a part in how much room they need, but even the lazy-plodders like some variety in their environment, so enrichment is very important, no matter how large or small their living space is.
I assume you mean it's a two-story hutch and the pop hole is the hole at the top of the ramp?
They are not likely to fall down the hole, but the best thing to do with multiple levels is to make the ramp shallower - less steep. Shop-bought hutches and cages tend to come with ramps that are too steep for alot of piggies. Also if you have a nice wide shallow ramp, if a pig does slip over the edge of the hole it's less likely to be hurt. I have a multi-story cage and I must say I have never seen any of mine fall down the hole between levels, but if they did they would find themselves on a gentle ramp. Having a tunnel attached to the ramp will make it safer and more appealing for the pig. You can buy fleece ramp-tunnels on eBay, they attach underneath with ties I think. I have sides on two of the ramps so that the pigs cannot fall off it, and on a smaller ramp I have a plastic-mesh tunnel fixed to it.
If you are concerned about space outdoors is it possible to keep them indoors?
If your kitchen is pig-safe then have you considered free-range kitchen-piggies? It's not for everyone, I can't free-range mine.....
The thing is as youngsters they tend to love running around, in and out of things and leaping about, sometimes play-chasing. They tend to build up steam and let it off making mad dashes around their enclosure. If you do manage to find a way of giving them more floor space it will allow them to do this, plus it will give more options for enrichment items such as tunnels, and hidie-houses, boxes and paper bags with hay etc. When they are older pigs are more likely to grump at each other if they're constantly in each others space, or perhaps even fight. Having more than one level can help with this, it does provide enrichment and a place for one to get away from the other, and as I say plenty or run time also helps a lot, but if there is any way to fit in a larger cage/hutch then that would be good.