If you're still open to ideas to explore...
These media container formats seems to allow including bitmap bytes as video frames.
- MOV container (Apple Quicktime) seems to support a PNG codec
AVI container (supports RGBA lossless codecs - see Lagarith & HuffYUV)
FLV container (supports both bitmap data and JPEG) : The bitmap codec is referred to a "ScreenVideo" but its just uncompressed RGBA information wedged between some 11 front-bytes (defines frame/tag header inc timestamps etc) + your bitmap data + closing 4 bytes (an integer confirming the tag size).
MP4 only holds MPEG codecs (so must the picture must be H.264 or H.265 format) : Are you using C++? I think someone made a keyframe encoder for H.264 so maybe you can use that code to supply thr final encoding (or at least end up with .h264 file that can be put into MP4 by FFMPEG or such tool)
Basically use OpenCV to handle whatever format you have, stepping through frame by frame and extracting each frame to RGBA then edit the image grab and either put that bitmapdata to FLV or use that Cardinal Peak's H264 encoder code. You dont need an FLV encoder just some way to write bytes defining an FLV file. Its so easy you can even use a hex-editor (obviously pasting in the long bitmap data where required)