Yeah, it’s oddly phrased. The first sentence restricts a true empowered item from having any other empowerments of another type, while the second restricts it from having any other empowerments of the same type.
That aside, personally, I think a restriction to one TE per person would potentially just lead to either people not wanting them, which robs ritual casters of the opportunity to use their “cool thing” or people playing stupid games with magic items.
As to your three points:
1) The residual flaw from a TE can last far longer than the 5 days in 1.3.
2) Everything about all the empowerments has always been about adding power, which is frequently checked in 2.0, but not exclusively.
3) Durations (of magic items?) are converted to a different system. Your one year item may last longer under the new system or you may burn through it in 6 months. It depends on how often you play.
Justification, perhaps, but not overwhelming.