There are no bands on the SE (1,2,3,4,5,8,12,13,17,18,19,20,25,26,29) that aren't also on the T-Mobile/AT&T X (1,2,3,4,5,7,8,12,13,17,18,19,20,25,26,28,29,30,34 ,38,39,40,41,66), so it wasn't that.
Both X variants support exactly the same LTE bands, so buying the other X wouldn't have helped. Japan doesn't operate any CDMA (that you get access to) or TD-SCDMA networks (the only difference between the models on the connectivity front) so the difference in connectivity you experienced is due to some other factor.
I was just in Japan recently with an X and had connectivity absolutely everywhere except during the ride up to Mt. Fuji, which is normal - the Fuji Subaru Line doesn't really have much in the way of coverage, but the stations do.
You also can manually change the network to one that has better coverage if necessary – my partner's iPhone 6s+ tried to use Softbank for most of the trip which did appear to have worse coverage than NTT. Switching them lead to better (perceived) coverage.