Ditto. I've complained about this on ResetEra in the past. (Sorry for the bump)
This has been on my TODO list of things I wanted to fix for quite some time now, but I hadn't had a stable native Windows install for about a year. I finally remedied that situation yesterday and took a look because I expected this one to be easy. Sadly, I don't have anything useful to share.
The analog stick swap works identically between the Dreamcast and original XBOX releases. In fact, the memory region where the setting is stored is nearly identical between both versions. I was surprised to discover that the behavior of the analog stick and Dpad are actually controlled independently, so you can have movement on both the Analog stick and Dpad on the Dreamcast / Xbox version if you want to. (But that removes your ability to look) On Dreamcast, the analog stick behavior is stored at 0C2562D5. If you're using DEmul, the equivalent address is 2C2562D5. With a value of 0, the analog stick looks around like the default. With a value of 1, the analog stick allows you to move / run. On XBOX, this is same value is found at 01A8DF89 in the emulator CXBX, I'm not sure what that correlates to on actual hardware. The byte before that, 0C2562D4 on Dreamcast controls the setting for the triggers. A value of 0x63 means the L trigger is for look, R is Run, whereas a value of 0x23 swaps it, L is R and R is Look. The same values are used on Xbox.
I figured since the trigger swap setting exists in the ports that I could just change the value and search for 0x63 or 0x23 then use the byte after it to flip the behavior of the right stick to movement. Sadly it appears that those same Look/Run values are not used for the trigger settings on the PC port of Shenmue II. I've also tried looking for that same memory region found on Dreamcast and Xbox by looking for other markers nearby and didn't have any luck finding it.
With all of the stuff that went unchanged compared to the original including leftovers, I'm actually surprised that I wasn't able to find the controller settings. I'm still under the impression that the underlying stuff is the same and they just slapped a brand new menu system on top so I was surprised not to find the control settings stuff.
One experiment that could be worth trying: I know people have managed to "convert" Dreamcast save data to work with the PC version. Has anyone tried to import the system file from the DC version (if any equivalent exists) into the PC version? It may be worth figuring out if they just completely axed the existing settings bits and replaced those. If so then it's actually feasible that they could have replaced the original control behavior logic. That doesn't mean it's impossible to bring back proper analog controls, just that it wouldn't be as easy as swapping the built-in flags and control mappings.