Ash,
Drilling holes in the end-plates is not an issue.
If you're confident you've got a good and consistent 360° spray out of a probe then pulling it through the length of the tubes will be fine.
My probe and spray-gun from RustBusters, who couldn't be bothered to supply advice/instructions/guidance, has never filled me with consistent delivery and 360° confidence, so what I will do with my frames - when they're ready for treating - is to do what I did with the Mini rear-doors, much as John suggests above.
I blocked off all the holes but one, then poured half a litre of warmed and thinned Waxoyl (maybe 10% white-spirit, can't remember) into the door.
Turning the door around and over in all directions gives a wonderful sloshing to everything and then you pull out the hole-bungs and let the excess drip out.
(And like our friend E600 says, if you park it in the sun in August you still get the occasional burp - note, this may be harder to reproduce in Edinburgh !)
This is sort-of how I did the doors on the Jag too, with an excess that I ran into all the intersteces and then drained off.
I've always thought that it was treating the key areas on my 1978 Mini Van to similar excesses in the early 1980's that has resulted in it being the only Mini I've ever seen that is still on original sills and sub-frames ?