So here is the thing, you are absolutely correct in theory and almost correct in practice depending on the source. With GSX2 modules, both GSX2 and GS-1 (with GSX2 modules) have exhibited slightly (very) better bass definition and sub bass quantity, which would suggest the original bipolar design had some limitation in delivering the required current for HE6 and similarly difficult to drive cans. HOWEVER, that minor added bass definition and quantity is offset by less natural rendition of the midrange, treble, perceived resolution and timbre quality, depending on the source components. With Linn as the front end, the JFET mk2 modules tend to do better overall if I am using something along the line of Audeze or similarly voiced cans. With Emm Labs as the front end, the JFET mk2 is simply a touch too hot for all my cans. The midrange took on a less natural tone, the treble is a bit too much for me to handle and that resulted in lower perceived resolution as now I am so focused on the treble and that masked some finer details elsewhere.
I have gone back and forth between mk1 and mk2 modules for GSX and GS-1 and those are my thoughts. For now, I have reverted GSX2 to GSX1 and paired that with Emm Labs and have GS-1 with GSX2 modules paired with Linn. The most shocking bit for you to think about - all the Audezes I own/tried in my system actually do better on Justin's very first dynalo amp (the one that he initially sold as a kit and later updated to V2SE) on singled ended than any of the company's later offerings, even the latest gsx2.
I am fully subscribed to the saying if it ain't broken don't fix it. I have heard similar "upgrade" (but regression in my view) with amps from manufacturers. So not every upgrade is an actual upgrade.