If you use the FLAC format for export, silent segments will already be compressed to next to nothing. For example, a WAV sample full of silence that would occupy 100 megabytes on disk will only take a few hundred kilobytes in FLAC format. OpenMPT already supports exporting to FLAC format, and Audacity can import FLAC samples just fine. FLAC can do everything WAV can do, except for 32-bit floating-point export.

Apart form that, it would be new to me that you can specify silence the way you imagine in any of the lossless formats that OpenMPT supports. Hence there is no way OpenMPT could do what you want it to do, as we cannot just invent an extension and then hope that Audacity adapts it. Adding support for Audacity project files would be way out of scope.

If you are concerned about wasted disk space, you can use FLAC format, which will losslessly compress the audio. In particular, digital silence will consume almost no disk space in FLAC. Note that you would be limited to integer PCM and you will not be able to use float PCM with FLAC, which might or might not be a problem in your use case.

Regarding automatically detecting digital silence and skipping such parts in the lossless output format, OpenMPT currently supports no format that would actually support such a feature.

I know of only one single format that inherently supports trimming digital silence, and that would be OggPCM. This format however is not widely used at all, even Audacity does not support it.

Having said that, it would theoretically possible to write PCM audio files with filesystem-level holes in them for parts with digital silence (which would avoid wasting disk space on NTFS file systems (but not on FAT)). I doubt the required engineering is worth the effort, though.