It depends on what you mean by bargain. I was offered a 10% discount when I sort of frown after learning that there is no tax refund at a shop (could that be counted as automatically, don't know). My fd and I have managed to talk RM owner's son into giving us a further discount on already 50% off items. If you offer to pay cash, some stores may give a small discount. This still works as they are mostly brick and mortar shops.
You usually don't ask straight up about discount. Get friendly and make conversation before asking. My fd got a small discount at Barnstomer. He had exchanged email with the owner before we arrived at Tokyo. Sometimes you get a token gift like OP. We got denim calenders, stickers and badges from shops like Lee, Schott, Dry Bones etc. We were given some Lightning magazines at RM stores.
And people do bargain at the many vintage stores. I have seen a customer getting a deal on a 50s vintage Lee Stormrider. My experience is that you do not do that in one of those stores which flip limited edition NOS sneakers.
Being A brick and mortar shop is a very good point. Other than doing a business，they see themselves as an artisan too crafting creations lost over time. Taking pride in their products and coming across supporters appreciating their craft, they could reciprocate with discounts and free gifts.
Was given a small tote but that’s basically the store’s promotion at that time. As I was dealing with the store manager who is most likely an employee there, I doubt he has that much flexibility to discounts or gifts. We’ve gotten really friendly to the extent that he was askIng for my instagram so I guess he would had given whatever he could have offered.