I see Passport Founder's Edition is showing Discontinued note, but can they still be used with latest firmware updates?
FE does run the latest firmware, yes.
What are the main difference compared with Batch2 in main board level?
There are some high-level block diagrams on GitHub (of course also the actual schematics), but the general architecture has barely changed:
Founders Edition:Batch 2:Case is much better in new model, as well as display, but I was asking about chips, processors and code.
You have to look more into the hardware repos I linked to, but from what I recall, the new hardware is only very slightly different. The codebase is now identical for both devices.