Unless they have a really good reason to do it any other way (which they usually don't), the best system is auto-saves + save anywhere. The auto-saves will act as a safety net if you forgot to save a long time, while saving anywhere allows you to save and stop at any point rather than having to push onwards to a save point or hope that the auto-save kicks in.

Anyway, as for recent Japanese games that have auto-saves..

Bravely Default 2 and Ys IX auto-save very often
Xenoblade 2 has auto-saves but very infrequent, I think it was after you actually finish a quest, be that a story quest or a sidequest
Nioh 2 of course, same system as Nioh 1
Resident Evil 3 Remake, unless of course you play on the difficulty without them. Can't remember how often it auto-saves, pretty sure it was often.
Atelier Ryza 2, though no idea how often it auto-saves as I haven't played it yet

Those are some of the ones I can think of from the last few years, at any rate. PC ports of the Trails games also tend to have auto-saves I think, but they're added by the westen porters, so..not so much a function added by the Japanese devs