Balloon flights have been done in lots of different controlled airspace, but are strictly limited to either letters of agreement pre-arranged with a local ATC unit to ensure that everyone understands if they are going in a certain direction what they may be expected to do if they are permitted into the zone, or secondly by prior arrangement for a one off "special" such as a record attempt or large event. This takes in some planning, but can be on a rolling basis so that if the weather is unsuitable for day 1 the whole plan rolls forward until the weather is good enough.
Bristol ATC have a local letter of agreement with the local balloonists and it works wonderfully - without the need for transponders! There are ongoing negotiations with other units to try to follow this example..