I would do this with Davinci Resolve.
It has a time code section specifically designed for this kind of thing. You can embed chapters into your movies then export. You can even cut out the intros if you want. You can set up a template and just add new movies and adjust the intro bookmark.
I bet there are movie enthusiast websites that provide timestamps for chapters. And I use the Media Player Classic app for video. It auto reads a folder and makes a playlist out of it and supports chapters with hotkeys.