Maybe cut the height down with an angle grinder, then use a heat gun to smooth out the roughened edge? Then you could proceed with the mold making. I don’t think backfilling your mold with more silicone would have a very high chance of success. Make sure you use a lot of mold release when casting silicone into silicone.

I think u/Armor_of_Inferno has the right idea though. 3D printed TPU seems like a much more sensible option for this kind of project. It would be great because you could change up the design and print new ones if your cat gets bored. I’d suggest a less ambitious and expensive first silicone mold for the mold making practice you’re after. Maybe even a smaller version of the slow feeder you’ve found, that’s closer to the end product you want?

Edit: here’s one made of silicone that might work, that only has 1” walls and is $10: https://www.amazon.com/DETOP-Feeder-Interactive-Eco-Friendly-Durable/dp/B01N1L7Z93