Re: "Silent" Ukemi
I think the easy (and probably the best) answer is to get Donovan Waite`s two tape series on ukemi.
Another thing to do is do various rolls and such that you normally do during practice and look and listen to when and how you make sound. Then you can explore ways to change them so that they are silent and still allow you to be safe and give both you and your partners good practice. For example. a lot of noise comes from the feet hitting the mat after a forward roll. It would be an excellent practice for you to dream up and try various ways so that they don`t hit. That would be much more productive than having someone tell where to put your feet.
As far as silent ukemi being good or not, the sound comes from something smacking into something else, right? To prevent injury, nage must lessen the power of the technique or uke must tighten their muscles to an extreme degree, or they must utilize special equipment (meaning soft mats.) None of this seems like a good idea to be done on a regular basis.
I`m confused by your example. By it, can I assume that you mean that silent ukemi can only be done in response to nage`s poor "architecture"?