Interesting - I own a 3-PU 5622, played an easy 2-3 dozen 5000-Series E-matics since they first came on the market, and the only times I found those problems was in the first run (before the changeover from Broad'trons -
the same PU's used on the Chinese E-matics and Streamliner Series BTW - to Filter'trons/Super Hi-lo's) and the recent Chinese production; while I don't doubt your experiences/impressions for a second, I've never personally encountered these issues in
any post-2012 MIK E-Matic - then again, there's bound to be a bad apple in every barrel...
By the same token I also own a 2013 6136DC White Falcon, and while the hardware is in fact generally better-quality (USA Bigsby; Space Control bridge that actually plays in tune unlike the '60s stuff; re-created early-60's High-Sensitive Filter'Trons with split-top covers, true-replica jeweled knobs) - FYI they both have modern sealed Grovers (Rotomatics on the 5622, Imperials on the Falcon) - and there's a bit more cosmetic refinement, there's nothing lacking in either tone or QC on the E-Matic that's been serving as my go-to gigging/home-practice guitar for the last five years. As far as resonance/sustain/thickness of tone are concerned, aside from the different pickups (Baldwin-blacktop Filter'Tron versus the TV Jones PU's fitted to most of the Player Series instruments) they're equipped with different-gauge strings - 10's on the E-Matics, 11's on the Pro Series (not sure about the PE models) - which IME make a
major difference in all the areas you cite; aside from using flatwounds on all my Gretsch instruments (I also still have the sunburst Double Annie I bought brand-new in 1964), I found I got the best results by going instead with 10's on the (25-1/2" scale) Falcon and 11's on the E-Matic (traditional Gretsch 24.6" scale). Frankly, that's what I like about the way the A/B comparison was conducted: same strings, same amp/same settings, straight guitar-cable-amp for most of the actual head-to-head (after the 15:00 mark), same licks - the guitars do all the talking with no extraneous influences, and you're free to form your own impressions...