Sorry but I have the opposite experience, although it will 'stick' to a pvc pond liner the bond is not strong, if it is rubber liner I cant say.
I spoke to Geocel, an English partner of Dow Corning and for pvc you have to use Dow Corning 794S. This does contain a fungicide from memory but I only wanted a little silicon in 2600 US gal so I was prepared to risk it and I got some but then found liner seaming tape.
This will stick to glass and liner and you could make a bottomed and 3 sided liner box and stick the box to your glass.
If you still want to go the silicon route GE makes a fish safe one but unfortunately I dont remember the exact name.
Incidently you dont have to fiberglass you can use an epoxy paint and I am sure this has been done in
http://www.fishcrazy.co.uk/cgi-bin/yabbfish/YaBB.pl .
The thread may still be there but a lot was lost a while ago when the server was hacked