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Basically, if you're asking, "Is FGO more popular than [insert gacha game here] in JP," the answer is yes. It's kind of ridiculous.
This^ lol Based on earnings alone, it regularly tops most grossing game apps list. Even effing bloomberg from all news site, decides to cover it last year (with a good amount of cringe) https://www.bloomberg.com/news/articles/2016-12-04/psst-sony-has-a-hit-that-s-as-big-as-pokemon-go-in-japan
Looking at Appannie, its still number 1 for today.