It was intentional that Nichiren offered only single item but now that I think about it, why not allow more. The locking was not intentional but fixed now too.
Yeah those two are dupes so that a daily run could get double the effect. Those two along with one other one in that vendor inventory are actually daily modifiers and not "normal" relics. And yeah, they don't affect the first level as the level is actually generated before the skill is given. Could probably fix that too somehow but doesn't seem like a big priority... :D
Multiple pylons do trigger on a single tile but a tile can't have more than two colors and that's why the red effect didn't trigger.
Good catch about the "created cards" not triggering pylons. Now they do! The depth issue of the starting tile after dying on a boss level is now fixed too.