Apple have sadly removed a lot of functionality from their server software over the years although they have dramatically removed a lot of the cost as well. So you are correct the Server.app does not let you delete a client lease from the list unlike the older Server Admin.
Turning the DHCP server function off and on may be a quick option but otherwise you may have to consider an alternative DHCP server. I believe the list of leases is stored on the Mac server at /private/var/db/dhcpd_leases hypothetically it maybe possible to stop the bootpd aka. DHCP server, edit this file, and restart it.
With regards to other functionality like defining Time Servers, this can be done but not via the GUI. You will need to hand edit the /etc/bootpd.plist file. As the name of the config file suggests Apple use the bootpd software as the underlying DHCP server but have hugely modified it compared to the original open-source version. You can find information about the DHCP options supported as standard by typing -
man bootpd
As mentioned functions like Time Server, LDAP server, NetInfo server (aka. WINS) are all built-in and you merely have to add them manually. Other custom DHCP option codes can also be defined for example to add support for a VoIP phone system however the format for doing this is not intuitive. In fact for custom DHCP option codes you ideally need to use a utility I wrote to help out.
See http://jelockwood.blogspot.co.uk/2013/06/dhcp-server-on-os-x-server.html
Note: I don't believe a Mac client would actually use the DHCP option for a Time Server but it will cost you nothing to try.
I have previously used this approach to add support for a VoIP system, currently use it to define a WPAD (Web Proxy Auto Discovery) address, and like you I am about to add Time Servers.
Note: Apple call WPAD - Auto Proxy Discovery.