The config from the current slot is the one which is upgraded/installed on the newly upgraded/installed slot. So if you ran the installation onto MD1.3 from MD1.1 the 10.1.0 config would be installed on MD1.3. Your customizations would probably not get copied during the config save to a UCS file as they're probably not included in a UCS by default. If you wanted, you could modify that though:
SOL4420 - Viewing and modifying the files that are configured for inclusion in a UCS archive
http://support.f5.com/kb/en-us/solutions/public/4000/400/sol4420.html
A hotfix isn't included as config. So you'd need to specifically install the hotfix. You can actually skip explicitly installing the base ISO if you select the hotfix and the slot to install it on. As long as you have the base ISO in the /shared/images repository, LTM will install the base version first and then the hotfix for you.
Aaron
Cirrostratus