From what I understand:
Adobe uses the MainConcept MPEG encoding tools. This is kind of awesome because Pandora uses a modified version of the MainConcept SDK, which means that generally speaking, stuff that's encoded by Adobe (with the right settings) should play fine on PB. The principal settings that someone exporting using the Adobe MPEG-2 encoder (in ME, AE or PR) has to change are:
Disable "Export Audio" (checkbox at the top)
"Quality" to 100
Field Order: Progressive
Profile: High
Level: High
Bitrate Encoding: CBR <---VERY IMPORTANT FOR SYNC!!
Bitrate: ~25Mbps for 1920x1080 30fps
The extension of the output file should automatically change to M2V, which is the default for elementary video mpegs. I generally also recommend: using 30fps where possible and setting the Aspect Ratio for square pixels.
2k is a problem though:
The MainConcept encoder in Adobe is configured to verify that the output resolution is set to a resolution that is in the documented MPEG-2 spec.
http://www.iem.thm.de/telekom-labor/zinke/mk/mpeg2beg/beginnzi.htm#Profiles%20and%20Levels(this document actually outlines a lot of the stuff about intra frames too.)
The DCI 2K 1.90:1 resolution is conspicuously absent from the list. So Adobe won't let you do this (unless someone knows a hack for it). The PB Media Encoder has the spec-confroming flags disabled, which means that it is boatloads more flexible for doing Pandora-y stuff with.
The only drawback is that there is a transcode during ingestion. Some people prefer to use the Adobe tools because it means that the transcoding can be done during export, before delivery. This is often a significant time (and space) saver, and may justify discarding 128pixels of horizontal resolution.
Audio: yeah, even in MC, you would want to do a separate export pass for the Audio (PCM WAV). Fortunately, exporting audio takes very little time.
cheers!