Well, Tanzra being a sort-of-anagram of Satan makes more sense than it being an anagram of Tarzan. (But then there's Satan and Santa...but I digress.)
Nintendo having shied away from religion back in those days is no surprise and there are many examples of that in that era. That era has certainly passed (or at least the reins loosened for older-age-appropriate games), with clear examples like last year's Bayonetta 2 (which Nintendo published) where Bayonetta violently takes down demons and angels in a journey somewhat reminiscent of Dante's travels in The Divine Comedy. You wouldn't have seen that in 1991! At least not if Nintendo had any say in it. If ActRaiser was rereleased or remade today, do you think anyone would notice or care if they changed all references to "Master" back to "God"?
What I find more offensive than anything like that is the removal of the simulation part (which I thought was what made this game special) for the sequel. I never ever did get far at all in ActRaiser 2 anyway, for some reason being unable to jump from a leaf to a ledge in Benefic. Very odd place to be stuck, tried so many times, still wonder what I am missing? Maybe I should watch a YouTube playthrough or something.
Anyway, I also was not aware that the Japanese version had differences in the layout. Differently designed enemies is not a surprise, but the stage design is another thing. I guess in my head I always imagine localizing departments to just be hacking the text, and maybe editing some graphics, stuff an amateur ROM hacker might do, not something more physical/structural (in the in-game sense). I'm sure I'm wrong but that's just an idea that's stuck with me for years.