Agreed. The nature of that advantage is not clear but what's clear is that they receive immense benefit from our dams, and they should be made to share the construction and maintenance costs.
BD has made all the efforts that any sane government could make to help India. It is Manmohan Sinhg's lack of initiative which scuttled the momentum. I think the utility of free passage through BD has very limited military advantage. Even if BD government gave us a signed paper assuring us the right of passage, tomorrow if we need to use the road to transport soldiers to troubled areas in NE or Myanmar or LAC, then it wont be the legal document which would be the bottleneck/force multiplier. Our enemy, (whoever we are fighting at that time), will always find ways to sneak saboteurs into Bangladesh and the only way to continue using the road would be through use of force, BD's legal and moral position notwithstanding. The legal agreement isn't worth the paper it's written on since BD doesn't have the military might to enforce it in case it is challenged by another power. We will have to enforce it ourselves.
The best way to overcome this is to base our strategic assets like ammo manufacturing units, ammo dumps, missile defense systems and other things to be built in NE itself, so we don't have to rely on transporting those things in the first place. That's the shortest path to resupplying our troops. Once that is done, the only variable that remains floating is the troops. We can add or remove troops based on the required force structure and it can be done without reliance on hostile terrain to transport.
Sign some sort of weapons/ammo deal with Myanamar to sell ammo to them, so that our factories and assembly lines stationed in NE remain active and profitable. When war breaks out, we can use these factories to supply our army.
Do a quick google search and try to find out the groups which are spreading disinformation, galvanizing negative public opinion and protesting against any attempts at river linking. Hint : Communists.