That idea does have potential to be honest. With 1.0 echo I don't think you'd even have to play as Elidibus to interact would you? You could be there and not be there at the same time, it even gels with Elidibus only sort of half-remembering you being there before you go.
I suppose the issue they've got there is that very few people are familiar with the 1.0 echo, while basically everyone is familiar with the concept of the crystal tower as a time machine. They'd have to lay some groundwork re-establishing it if they wanted to use it that way.
With a few tweaks they could have twisted the 'echo reading the land' ability into using the echo on the tower to travel back and forth. Would have to be done pretty carefully though.
Yeah, it was 100% not all planned from the start and it shows. I'd forgotten about XVI, now that you've mentioned it though it will be interesting to see what Yoshi-P can do with a game he has control over from the beginning.
The raid helps a little in this regard at least, establishing that while we TP for gameplay purposes, in-universe we have to back to the tower and use the portal there.