"image overlay" is in the preset list of the Video Processor plugin. It can be used to overlay images and also other videos. For logos, you should create transparent PNG files for all the designated video frame dimensions you are planning to use it on, for example, if your source video is 1280x720 HD, you should use a 1280x720 version of your transparent logo PNG (with the logo already located at the final position in the PNG) so that the overlayed logo doesn't require any scaling or panning at all. Else, the output render will suffer in terms of resolution.
While Reaper has no problem at all mixing different audio sample rates and bit depths on the fly or during rendering, the same is not true for video. If you are mixing videos (or logos) with different dimensions or frame rates, you'll get artefacts in the final render.
For all of your other requests, I think the answer is no currently.
To have both a video and an audio track to process separately in Reaper, I'm duplicating the video track (showing the audio wave form) and then I glue the copy to make it audio only. You could also use a media stream extraction utility that de-muxes the video and the audio from the original interleaved video file. Occasionally, I'm using "Free Audio Video Pack" for this.
If you wanna replace the audio track of a video without touching the original video quality, open the video file in Reaper, edit the audio as required, make sure that the new, edited audio has the exact same length as the video, render the new audio only and then use AVIDemux to replace the original audio stream in the video with the new audio file.
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