There are several designs with wing, tail and thrust lines in line, and some seem to fly well. Mike Pratt's P-Force, now ARF'ed by Sig, is one such model that seems to fly quite well. Mine, built from his short kit several years ago, does OK. Some feel that behavior around neutral in straight flight is better with the stab not aligned with the wing chord, since it avoids the turbulence and perhaps some down-wash from the wing.
Whatever the height of the horizontal tail, other dimensions must be attuned to it, including the longitudinal c.g. location. Downwash from the wing can affect the elevator's neutral setting and input, perhaps the desired stab incidence and/or down-thrust, and definitely changes the neutral point of the aircraft. The vertical center of drag is affected, since the drag on a raised stab tends to pitch the plane up (as does gyroscopic precession), to balance drag on the landing gear and a raised thrust line, which tend to pitch it downward. It's pretty complicated, but I think that except at the highest levels, c.g. placement and elevator setting are probably sufficient to trim a plane for any reasonable stab height. You should do a search on SSW Forum's archives, where this question has been discussed in detail more than a couple times by some of the best minds in CL stunt.
One thing thing I believe true though is that you cannot make the plane symmetrical even with everything in line. Symmetrical architecture is no more aerodynamically symmetrical than the best balanced/trimmed "conventional" designs. I like the in-line idea, but have no expectation that aerodynamic adjustments can make up for P-factor, gyroscopic precession and even landing gear drag/polar moment. So I think that regardless of how well anyone thinks "inside" maneuvers match "outside" maneuvers, they really don't. The human mind and senses adjust in a marvelous way for physical asymmetries. For instance, raising the stab may avoid wing/tail interference to some extent upright or level, but somewhere inverted or doing outside maneuvers, those wakes will interfere. Still, I have to admit that my present project started out fully "in-line", but I raised the stab before completing the fuselage work. Oh, well...
SK