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I have Dante Labs WGS kit for which, using WGS Extract, I created an everything kit for GEDmatch. When I uploaded it as other since Dante Labs is not an option, it was identified as being "23andMe kit type V3". I did a one-to-one with an Ancestry kit of the same person and got Total Half-Match segments (HIR) = 3559.9 cM (99.260 Pct) so clearly GEDmatch has thrown away the portions that are not in 23andMe v3.

Here is snapshot of WGS Extract dialog for choosing what autosomal to generate:

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Now there are tier1 tools at GEDmatch where I could combine multiple kits to make a super kit, so must I instead use WGS Extract to create a series of individual kits, one for each company and each version of that company, and then put them back together again in a super kit or, preferably, can I avoid all that overhead and somehow upload the everything file directly? Perhaps by selecting something other than other such as one of the list that is a WGS sequencing?

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