Couple thoughts:
Get a MiniDSP 2x4 and Umik1 and learn how to dial your Subs in with Room EQ Wizard.
or
Daisy chain your Subs if that is an option.
or
Y split as you suggested.
The last two will limit you more. You will be reliant on luck finding good acoustics, and luck hoping that YPAO does a good job.
The first option will cost more, in time and money, but once you learn REW, you will be in control of your Subs and can tell YPAO to kiss your @$$.
Regardless, I am not experienced with YPAO, and only know by anecdote and hearsay that it is not the best. That said, the equidistant solution would be your best/safest bet. Be mindful, the room acoustics could end up having one, or both subs in poor locations, and you will have little to no control over that. (just short of moving both subs to maintain an equidistant relationship.
Hope that make sense and helps.