Waterproofing structures like this is perfectly possible but meticulous planning, detailing and attention during the build is essential to avoid mistakes. Suggest you do a section detail through the wall/floor to show us how you plan on building/waterproofing it and post it on here for comments...
I'd be inclined to try a food safe silicone. Seems like the OP may like to continue using it for sentimental reasons, for which its hard to criticize. Some grumpy feckers in this thread.
Drawing packages have their uses, no need if the builder is highly competent and reliable but otherwise they can form the basis of a contract. The forum is rife with people coming unstuck because their contract with their builder is full of holes.
Just fix one of these or similar to the back and one on the underneath with some suitable screws, IKEA stuff is frankly sometimes a bit naff and need repairing, then move on with your life. Forget about filler...
The conservatory company is wrong (and more than likely they know it only too well) but I too would just do it but build over the drain by the books - that is adopting all of the measures necessary as if you were doing a build over.
That said I would never build a conservatory anyway, they're...