(One question per thread, please.)
[ul][li] Checkbox mode in Opus is used somewhat differently to that in Explorer (ours predates theirs and was never meant to solve the same problem). While ours is there to allow you to display files in the preview pane while still building up a selection, Explorer's is more about making it easier to Ctrl-Click things with only one hand. You can do that in Opus by clicking files with the middle mouse button (assuming it is set to be a standard button), without needing to use checkbox mode at all.
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[li]If you configure the Movie plugin you can specify how far into the files it seeks before taking the thumbnails. There may also be problems with some codecs/demuxers, since it is at the mercy of the installed video components. Note that it uses 64-bit DLLs while a lot of video software uses 32-bit ones, which can be another cause of differences if different components are installed for each "bitness".
If you turn off the Movie plugin (or disable its option to generate thumbnails) then Opus will rely on Windows to generate the thumbnails, and you should get the same ones that you see in Explorer. (If the plugin is disabled entirely, movie playback will fall back on the ActiveX + Preview + Office + Web plugin, which will most likely use an embedded Windows Media Player viewer for the viewer panel.)
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[li]Drag & drop events can be configured, but that's best discussed in a separate thread.
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[li]Images toolbar: Turn it off under Preferences / File Display Modes / Toolbars.
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[li]Max thumbnail size can be increased under Preferences / Miscellaneous / Advanced: max_thumbnail_size but note that increasing it means more memory and more disk space is used (of course).
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[li]Colors can be changed under Preferences / Display / Colors and Fonts. Most programs default to a white background because Windows tells them to. It's Windows that default to a white background rather than the programs (in general). But Opus lets you override it.
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[li]We used to have animated avi thumbnails, many years ago, but it did somewhat horrible things to the disk when displaying a screen full of videos all at once.[/li][/ul]