I was in Japan last month, tipped 4 times, once it ended up awkward with the waiter insisting me to take it back, the other 3 times they accepted it gladly and thanked.
Please keep your tip customs out of our culture. Next time just say thank you several times to show you appreciate them.
I wouldn’t be surprised if they are being instructed to accept tips, in order to keep the customer happy.
Many of them end up in hospitality, especially in touristic places, due to different reasons, but very importantly, immigrants from south Asia generally speak English fluently, something Japanese people rarely do.
I've seen plenty of "japanese" restaurants in Shinjuku where not a single member of the staff was japanese.
Another place where you're gonna see plenty of immigrants are all convenience stores.