The 3 attachments listed above are not really necessary. They are added just to document the process, and keep track of the encoding parameters. You can remove them if you wish. (Note that if you define some cover art images in tab 4, they are also added as attachments. And, if you have requested to convert at least one subtitle track to 3D, a zipped archive with the 3D-planes is also attached, so that it will be easy to convert a new subtitle stream to 3D if necessary.) Anyway, all these files are very light, so IMO it is worth keeping them.
And yes, the development of tsMuxeR has stopped (again) and I have included the latest version that works correctly. If you go to Help -> tsMuxeR Version, you'll see this:
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BD3D2MK3D
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Network Optix tsMuxeR. Version 2.6.9. www.networkoptix.com
WARNING: Do NOT use v2.6.11 or v2.6.12 as they have a big bug with the time codes of the subtitle streams of some BDs. The last known good version is v2.6.9.
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I don't think that v2.6.10 has been released officially, so you should stick with v2.6.9. Anyway, the improvements in the two last versions are related to the muxing process only. Nothing has changed for the demux, except the new subtitles timecodes bug.