This is a maybe...more practiced people here than I.
We use our x-pen for specific purposes: Bed time for the two pups and if I have to leave for the day for the pups. (the adults are left to run the upper part of the house near the x-pen) What they do for sure when I'm gone during the day who knows; however, at night... they quiet right down, go to sleep until they hear one of our alarms go off in the morning. (At night we completely cover it with a sheet (not so during the day) - We never put them in it when we're home (our thinking: why would we?...they run the upper level of the house when we're home) So I think they realize when they're in there, they're in there for a reason thus why fuss about it? Now I realize having two - they have each other, but it wasn't always that way, that was one's routine before the other pup came, so I don't think it's having "company" that makes all the difference (though I'm sure it helps).
I think you have to think "safety" --- before we got an x-pen whenever we had one pup we babygated the bathroom door and that's where it stayed while we were at work. If they fussed (sad as it is) while you're gone at least you know yours will be safe. Dogs adjust, some it takes awhile longer, but in the end they adjust.
I think if someone has to be gone a lot having another pup near same size/a few months age difference/similar temperament can make all the difference, but I know a second pup isn't always an option.
After all that my suggestion is (I get on a roll sometimes
): you've introduced the x-pen, use it only when necessary, provide food, water, safe treats and toys, washable potty pad, comfy blankets, maybe a donut type bed and the pup will accept its routine in time.