I can think of two ways to change exposure over time and they both involve interalometers and servo motors:
1) connect interalometer to your geared and declicked aperture ring (easier with a cinema lens) and animate the iris over time. Downiside: change in DOF over time, but may be moot if lens is at infinity.
2) use a fader ND and rig a servo and interalometer to it. Downside: an extra filter and at least 2 stops light loss, but not a problem for long exposures.
Using AE modes is possible, but yields unpredictable results and you don't have much control. If you're at aperture priority, it will adjust shutter speed or ISO, but these are in third stop increments at best and will not be totally smooth in the transitions (but might be close enough for government work).