Hi Dalton,
I like to give you some answers to your questions.
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Do most Calibre users with embroidery libraries have "real" proprietary embroidery software to extract the metadata, especially for complex file formats like .pes that contain a .pec embedded within it?
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I do not know if there are calibre users that do as well embroidery.

It depends on what they are doing. If a user only stitch commercial designs, they buy an embroidery file and stitch it with the machine. They are able to change the size by some % within the machine but are not able to make general changes on a design. They sometimes use free of charge tools like Wilcom Truesizer, Bernina Artlink and some other to convert a file format from one to an other format. In my case a Bernina and I use ART, EXP and EXP+ (a variation of the commercial melco exp format with two additional files for thread colors and a low res picture)
If they want to do more, they need most time proprietary embroidery software. There is only one free software called embroidermodder what is more or less a basic develpoment. Since one of the two major contributor died in a tragic accident there is only a bit maintenance since long time (
https://github.com/Embroidermodder/Embroidermodder). It is as well a good starting point for programmers as you can find there some information for supported formats.
So most people need to buy proprietary embroidery software if they want to do more than stitching out a design. Not a few buy software from the same company the machine came from because of the capabilities for a fully supported native format and, well because it was a small market with only a handful player around the arena and the seller like to sell more expensive software...
Beside the main actors in the business there are some small companies with own development. Sandscomputering, Balard and some more. The entry costs are for not main actors a little below the level of main actors 150+. If you like to do create embroidery yourself, the cost will increase very fast to huge numbers depending on the functionality .5k to 2k in home embroidery software and in commercial area starting by 1.5k to 20k+ per workstation. The other problem are the file formats. Most of them are not public and the companies who own the formats do not publish any information. Known information about some of the formats are reverse engineering data based from somewhen in the beginning 2000. They differ between versions within a format, the manufacturer and the kind of information a embroidery file contains. I used the wording "native format" some when before. Embroidery files in general you can sort in formats that only represent stitch information and formats that represent outline information. The last one are complex files with object outlines, object properties and stitch data. Newer formats supports additional information like different colorways for a design, project information like metadata and so on.
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If they do, does their software create a text file with the metadata for each embroidery file format that can be imported by MFI to update Calibre custom columns? Or a .CSV file that could be imported to do the same thing, but en masse for an entire embroidery design library?
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Not really. With commercial design files you become this data as separate information in different formats per design. These are called project information/files and/or thread charts as picture, paper, text file or pdf. No standards.
Data en masse. Well, I know only one software but that is a professional solution. For a low budget or free solution I don't know if there is other software available what can create these kind of data. I haven't seen that up to now somewhere around. Maybe other user can give you an answer.
I am just thinking a bit around. Maybe you or someone else have an elegant idea to extract the data from a pdf project file. Then there is a solution thinkable that match a lot of formats without the need of decode file formats. The user only needs to create a project sheet with a free tool.