Silicone does not stick to plastic very well. Probably will be OK if you absolutely do not flex the pair of bottles, but the least disturbance and the silicone will pop off.
Here is an idea that you will have to research a bit.
My father made a toy for the grandchildren. It was 2 bottles of 2 liters each, connected at the opening. He partially filled the system with water and glitter. You would swirl the bottles and turn them upside down and watch the whirlpool as the water swirled from the upper bottle to the lower.
Here is my point: The system never leaked! There was some sort of tubing connecting the bottles. You might find it in a 'science for kids' sort of store, or a hobby shop. I have no idea even what to ask for. Good luck.
Next idea: Wholesale irrigation store near me gives away damaged pipe free to whoever wants it. It may have been run over, bent or whatever. For the amount of good pipe you would use, (a foot or so) you might ask at places like Ewing, Horizon, Water Savers, John Deere or who ever is near you.
Yes, you then have to buy the fittings. However, they will not leak, and you can include something that will adapt to the tubing from the pump quite easily. Stock item, not DIY.
I remember making those "tornado in a bottle" things in middle school! Maybe it unconsciously inspired me to make this lol. I found a link to how to make them and then found this:
It is a small piece that connects the bottles together. Hmmm, this might be worth getting if it doesn't leak! The only other problem is you said silicone doesn't stick to plastic well so maybe instead of relying on only silicone maybe I can get a bulk head to attach at entry point of hose from water pump into first bottle. I would only need one and then just silicone around that to make sure it seals properly. I don't mind scrapping the water bottles, but I still want it to look like clear tubes so the filter media is visible. So pvc is kinda out of the question for me not because it won't work well (it would definitely be easy to make water tight) but just because I have a particular image of how I want it to look aside from function lol. I know I'm hard headed! I would prefer glass tubes of some sort but not sure what is cost effective and easy to manipulate. Back to the drawing board!