whatever the bhartis do in Afghanistan is their own business as long as it doesnt interfere in Pakistan --and for that reason surely we'll have some close eyes on their moves....business is business, the media and other individuals like to hype this whole thing up -- that Pakistan will suddenly raise hue and cry over it. Dirt cheap indian labourers have been in Afghanistan for well over a decade now, mixing concrete and working on roads and some other projects here and there. india does have some 'interests' there -- some financial and of course some illegitimate things which they will be held accountable for --such as using Afghanistan soil in a hostile fashion against Pakistan.....those are generally things that don't (and can't) go un-answered.
as for the routes -- well they have a working relationship with the Uzbeks so maybe they can coordinate with them. I'd be very surprised if Pakistan granted hindustan the rights to use its highways up till the border with Afghanistan. In fact, I personally wouldn't bet on it. High toll or no toll at all. It's a national security issue. I don't think the indians have proved that they can be trusted; same way they argue that they don't trust Pakistan.
can't change geography though!