I'm not sure if this way of thinking makes sense.
I was with Belgravia last year. The recommended dose was indeed 1ml per application.
If you use the 2.5ml of 5% Rogaine over your whole scalp, what you will end up with is more of the less concentrated topical solution. The overall amount of Minoxidil making contact with your scalp may be the same, but there will be a larger amount of fluid diluting the strength.
I would say if 1ml is the amount you feel would cover the area needed, stick to the higher strength one and use 1ml only.
Having said that, some don't seem to correlate anything more than 5% strength with more significant gain. If you're not suffering from the sides, go for the stronger one.