Why are there missing frames in the Vegas Pro editing timeline?
Vegas is not showing you the actual framerate based measurement. Instead, it is showing you 30 fps Drop Frame Timecode, which exists for compatibility reasons and does have to do with NTSC video.

For purposes of alignment with ffmpeg, switch your display to SS.mmm i.e. fractional seconds rather than SMPTE timecode. No need to change the project framerate.

Right click on one of the times at the top of the timeline and you will see that SMPTE Drop is selected. You can change that to "Time" or "Seconds" for a convention that FFmpeg will naturally understand.