If you drill the hole small enough, you don't need silicon to seal the hole.
When you pull the tubing through, it flexes, and gets narrow, when you stop pulling it returns back to it's original shape, and totally fills the hole, if drilled properly.
I've found this works well with silicone tubing, better with clippard tubing, and not as well with the vinyl.
I use this technique on all my bubble counters (3 of them) for use with pressurized, and a CO2 diffuser, and pressurized, and a CO2 reactor.
Also, I cut it about 1" above the cap and that is where my check valves go.