According to nugatory42 and the light novels behind it, that anime chapter in which he said the hourglass was his deepest wish seems to be true, part of the actual canon. In my interpretation of that, being it the skin of his strongest desire, I think it represents what you said, the promise he made to Alma.
As for being still able to see lotus flowers, I think he doesn't right now, that his innocence, being it all about illusions (all his powers are called something illusion something), enabled him to see them. He just had the extra nutshell of Woman!Alma chasing him around.
Yup, to me it souds like that, that Mugen is saving itself for its master, so nobody can actually touch it (also, it was surprising to see that the rust shape seems to look a lot like the wing covered version of Kanda's innocence). Cross, to me, for what has been said above, seemed to reject the innocence or perhaps Hevlaska lied. We are assuming that Zhu Mei lied about Kanda being dead to protect him, perhaps Hevlaska did the same and is part of the third front.
As for Tim, I think it can contact his master properly, it does not want to either due its personal reasons or because he hasn't be ordered to do so (I don't recall if at the manga Allen had to find out that Tim could find its maker on its own, I have been watching the anime because I never saw it) or because it has been ordered to not return to Cross after a particular event or certain time. To me, Tim always allows Cross to know about Allen's whereabouts and actions in order to keep him informed about how close he is or not of losing it to the 14th (If I was Cross, after finding out Allen could turn into a Noah, I would have that beansprout surveilled (?) a lot) that's why I also think it can find Allen anywhere he goes.
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As for being still able to see lotus flowers, I think he doesn't right now, that his innocence, being it all about illusions (all his powers are called something illusion something), enabled him to see them. He just had the extra nutshell of Woman!Alma chasing him around.
Yup, to me it souds like that, that Mugen is saving itself for its master, so nobody can actually touch it (also, it was surprising to see that the rust shape seems to look a lot like the wing covered version of Kanda's innocence). Cross, to me, for what has been said above, seemed to reject the innocence or perhaps Hevlaska lied. We are assuming that Zhu Mei lied about Kanda being dead to protect him, perhaps Hevlaska did the same and is part of the third front.
As for Tim, I think it can contact his master properly, it does not want to either due its personal reasons or because he hasn't be ordered to do so (I don't recall if at the manga Allen had to find out that Tim could find its maker on its own, I have been watching the anime because I never saw it) or because it has been ordered to not return to Cross after a particular event or certain time. To me, Tim always allows Cross to know about Allen's whereabouts and actions in order to keep him informed about how close he is or not of losing it to the 14th (If I was Cross, after finding out Allen could turn into a Noah, I would have that beansprout surveilled (?) a lot) that's why I also think it can find Allen anywhere he goes.
*hugs*