yes you could do it by using surface fillets. but beware, they are a little bit tricky. make sure you have the 2nd pipe intersecting the first one completely. because in one of your pictures i saw that both pipes had the same scale and the open end of intersecting pipe wasn´t completely inside the other.
damnit! this becomes really weird right now.. I show you what i mean.
see pic
if you want the circular fillet go all around the intersection maybe scale down CVs from the end of the intersecting pipe.
everything starts and ends in the right place at the right time.