you see services.localhost.net removing all modes because it is actually the ircd that is removing all the modues after having been told todo so by services (so source is services.localhost.net). This means that services only has to send 3 commands to the ircd (remove all -o's, -a's and -q's) instead of sending every single mode change for every singly user.
Botserv bots are also deopped because to the ircd it s a normal client and it s the ircd removing all modes so services can't control it unless it would send out every single mode change.
If the ircd doesn't support svsmode_ucmode, services have no other option then to send every mode change to the ircd itself and then you will see either chanserv or the botserv bot doing it. This means however more work for anope.
So theoretically you could make a protocol module in which you disable svsmode_ucmode and anope will set the modes itself instead of letting the ircd handle it. However modifying the anope source is not supported here and mean you will lose all support as we cannot be asked to support bugs you may have introduced.
