Do you have any written evidence of this? (eg. website/URL)
I personally haven't seen any written evidence of it (and I've read a lot). However, if Lindsay Craig has said that (and I have no reason to disbelieve EZY that he did), then we can probably assume that it's pretty reliable information.
Would it then count as 2 attempts if for example you failed at stage 1 the first year and failed at stage 3 the second year?
Since EZY said that you can only "apply" three times, it seems to imply that it doesn't matter how far each application subsequently goes. On each occasion it appears that it'll count as one of your three shots.