ffmpeg works really well for this. I have also been making time-lapse movies for over a decade, starting with using just Quicktime Pro 7 to combine the images into movies. Later using various other tools. Now I also use ffmpeg, and want to keep track of exactly how each movie is put together so looked for a way to script each movie. Now I use ffmpeg-python (not a lot of recent updates, but just works) to steer ffmpeg, with my own time-lapse specific Python package https://pypi.org/project/time-lapse/ to assemble the movies, and for each movie I have a single script which describes which frames are part of it and how they are combined into a movie; https://github.com/153957/time-lapse-scripts
I am quite happy with the setup, making it easy to recreate movies in the future from source, but at higher resolutions or different codecs.
https://fosdem.org/2026/schedule/event/FVQVTA-freesewing/