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I'm talking long term here - clearly in the short term the answer would be an emphatic no. (massacres and all around destruction)
However, say after a successful 2nd Mongol Invasion of Japan in 1281, Kubla Khan destroys the Shogunate, and subsequently unites all the desperate Japanese clans under a tributary Khanate. Then later, just like the Yuan Dynasty, the Mongol regime collapses.

Would Japan have been better off in this ATL compared to the years of strife and infighting that followed it's victory in OTL?

Some thoughts:
This pretty much butterflies the destruction of the Sengoku period, as well as the isolation of the Edo as both the legitimacy of a Shogunate and the importance placed on Feudal/Clan rivalrys would also certainly disappear post-Mongol regime. Also, as an integrated part of the Pax Mongolica, trade and cultural exchanges would most likely flourish during this period.
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