I work in and with the broadcast community. We work primarily in three formats: 720p60 (59.94fps), 1080i59.94, or 1080p60 (59.94).
After Effects CC 2017.2 (v 126.96.36.199) does not have a composition setting for progressive formats. For all HD formats, the options show 23.97 or 29.97 as the maximum frame rate. If I make a change to 59.94 or 60 to match the actual format I need, the composition is considered a "custom" comp and will not output as a legal HD format using the render que.
In response to Rick Gerard's responses to other questions, I need to use a 60fps (59.94) format because the switchers, broadcast media servers, and replay machines need to see a true 60-frame progressive format. Or interlaced at 1080i, which works out to 120 fields to make one second in the 60fps format.
Quicktime animations (RGB+Alpha), with audio, are needed for many of our pieces - transitions, interstitials, overlays used in switcher still-store based keys. Having to double the length of an output to get the timing to be correct is not optimal as then audio is wrong. Or the media server (a For-A Insight server) says the format (29.97fps) is invalid for a show being produced in 720p60.
Is there a plan by Adobe to address this issue?
I don't understand the problem you are experiencing. Making a custom composition shouldn't prevent it from rendering out properly.