Ana The imagination boggles. The poor man could fall out of bed!
It is not the size of the beaker, it is the angle of entry.To dangle something in water, the container has to be held upright, or the water will all spill out. The penis is joined to the pelvis more or less horizontally. In droopy mode, a fair bit of it will dangle in the water, but there will still be a bit at the root left undunked. That bit presumably came into contact with the same "contaminants" as the tip.
If he is so fussy about cleaning it he would be better to wait a few minutes and wash it in the bathroom - or share the bathroom. As someone said on MN, after what they have just been doing, why balk at sharing a bathroom?