When I 1st began using my BJ, (Dewalt, 1990 or 91 still have and use the same ) I had constant problems with alignment. As I spent time trying to figure out what I was doing wrong, I improved the results to the point where I no longer have issues worth mentioning.
Finish lumber from the Lumb.Yd, IMO, has a much higher quality and quantity than the big box stores. That said there is still much lacking in the product supplied, most is mass produced plain sawn, albeit kept under cover it's not climate controlled. The mill cutters get dull and misaligned and it shows with scalloping, chipping and surface waves.
Minus using an unsafe tool which is also human error, all problems can be traced back to human error which accounts for most or all of the problems with glue ups and in particular BJing. Most stock is crowned, hooked and uneven in dimension. If one assumes otherwise and just cuts up the stock for a glue up, regardless of diligence in the BJing process there will be dissatisfaction with the results.
The stock requires further milling to make it suitable for jointing and glue ups. Uniform dimensions and crown minimization by ripping pieces into manageable units, surface planing for uniform thickness, edge jointing to square the sides up.
For me once I began making the biscuit cuts with the stock elevated off the work bench or extended over the edge the rest of my inconsistent mismatch problems disappeared. I had wondered if I or the table was forcing the jointer to tilt ever so slightly as I pushed the blade into the stock. It was either or both, I never figured out, it was an inconsistent error, none-the-less it stopped once I removed the possibility.
Its wonderful when a large piece of lumber can be milled and utilized, but that doesn't happen often with new wood.
Work smart not hard!
Never bite the hand that looks dirty