See http://www.rpm.org/api/4.4.2.2/triggers.html for triggers that should be run later.
>deletion of files that were in the old RPM and not in
>this one happens after that, so the S99webmin links are lost
Yes chkconfig is strange. It's redhat. insserv does not do that - which gives me S10webmin here, so the removal of S99webmin is a no-brainer.
As for chkconfig, I would suggest that you change the priority from 99 to 98.
The loss of the S99webmin links when upgrading isn't really a chkconfig issue - rather, it is due to the way RPM cleans up old files when upgrading. So iniserv won't fix this.