Is there a single catch-all-features tracked music format?

Note: I'm an OpenMPT/libopenmpt developer and have worked on code dealing with module formats for more than ten years.

The quite simple answer to this question is "no". Not even the IT format, as suggested by mr_lou, is a viable superset of any of the mentioned formats. There is no format that does everything all the other formats do, and in particular among the formats you mentioned, .sid is the odd one out because it is not a tracked music format (it contains program code to execute on the C64 or emulator). Just among the formats you mentioned, each of them has unique commands not supported by the other formats:

• MOD has Invert Loop, which is rather unique to this format
• Playing S3Ms the "canonical" way (i.e. how ScreamTracker 3 would play them) is incompatible with IT in several ways, because it handles effect memory differently.
• Most people would believe XM is a subset of IT, but IT lacks some commands that XM has (e.g. Key Off or Set Envelope Position).
• Historically there have been some formats which tried to achieve what you want to achieve (e.g. MikMod's internal format, or BWSB's GDM), but they really are not supersets of all formats, and more realistically just model the capabilities of MikMod's or BWSB's internal workings.

You could continue this list with about any combination of two module formats and you will always find something that is done differently or is not supported by one of the formats. Each format and player has its own quirks which are unique to that format. Converting between those formats is always a lossy process in the general case. Please do not convert modules to different formats unless you absolutely must.

About the metadata issue, it would make the most sense to store this metadata separately from the file, because most module formats have poor metadata support, and embedding custom metadata is not always possible. This could for example be solved with a database like the STIL database for C64 SID music that comes with the High Voltage SID Collection.

I believe a viable solution to your problem is not to invent yet another container format to possibly contain every tracked music ever, but to have a standardized tracker music database and a player that can handle a wealth of formats (e.g. by combining libraries such as libopenmpt, UADE, reSID and some others). There are various players that can be extended with plugins (such as XMPlay) which do a great job at this. Currently in the works is also a modern reincarnation of HippoPlayer, which aims to be able to play almost any tracked music format, and in the end also provide rich metadata, possibly through an external database. You can see the progress of this project here: https://github.com/emoon/HippoPlayer