The only thing I can currently think of is to *exclude* these features
from the base_41 update site [3] so that only the older version from [2]
will be included.
This is basically the process I used to build JBT 4.1.0.1 - I excluded
everything from jbosstools-central's site/category.xml except the
feature which had actually changed [4].
I don't find it very easy to deal with picked dependencies on the
producer's side. Choosing dependencies is IMO a responsibility of
the consumer (JBT aggregator).