Some may wish to argue this, but I do feel that a slower cooking yields a more tender shoulder. Being a small 3lb piece of shoulder, I would be inclined to believe that 225-250* chamber temp is too high to produce this same tenderness. My typical pulled pork smokes with whole Boston Butts or Picnics range from 18-22 hours cooking time, while I have had some take over 25 hours.
That said, by your own comparison alone, your crock pot is yielding a more tender pork after 2-3 hours longer cooking time than you would smoke it in the Egg. My suggestion for the Egg would be to start your smoke at no higher than 225*, and reduce your temps to around 210-215* within 90 minutes and hold it there for 4-5 hours before bringing it back to the 225-230* range. This should still pass through the internal danger-zone temp of 40-140* in 4 hours (a smaller boneless butt may have a cavity in the meat so should be treated as compromised muscle). Dropping the temps back will slow down cooking quite a bit...possibly taking somewhere in the 10-13hr range to reach 200* I/T. Foiling, BTW, speeds up cooking at the cost of softening the bark, and quite possibly in your case, at the cost of tenderness. I haven't foiled my butts or picnics for pulled pork in probably close to 3 years, and I must say, foiling seems to be highly over-rated, and quite possibly misunderstood by many. The extra wait without foiling to finish is more than worth it in the finished product...unless you hate bark on your meat, that is.
Foiling with a towel wrap to rest with a smaller cut as you speak of may still be necessary to allow redistribution of the interior moisture, but with whole butts and picnics it's not needed...I just place the pork on a rack in a pan and cover with a clean towel to rest...this lets the bark breathe with minimal contact instead of steaming and softening under the tight wraps of foil. While it doesn't hold it's heat quite as long as foiled and towel wrapped, it's long enough to do the job and still be piping hot for pulling after ~3 hours.
So, get it through the danger-zone temps in reasonable time, but cut the heat back beforehand and let it coast through and begin slowing down so it doesn't cook too fast to not melt the collagen in the shoulder meat...when the collagen melts, you'll have tender pork shoulder. And, yes, some will argue that a there's nothing wrong with a hot & fast pork shoulder for pulled pork. I can only say that I've done one that way once...I puled up the thread...started more or less low & slow, then pushed it hard, with a 7.5lb whole butt...let me just say that I won't ever do that again, because as you have been experiencing, it would not pull...it was difficult to even get it to shred...no, I won't do it again.
Here's that thread...results are in post #8:
OK, I've rambled on long enough...it's late, and I'm tired...probably to tired to make much sense anymore, but, that's the best info I can give you on a butt smoke that won't yield a nice, easy pulled pork.
Catch you on the flip-side.
Oh, one last thing before I do my eyelid inspections: be sure your temp gauge or probe is giving accurate smoke chamber temp readings...nothing worse than thinking your smoking @ 225* and the actual temp is over 275*...more on this later if you need info.