Sorry, we have only linked on Lead, not on Company. I've found this but likely you have already seen it: https://docs.marketo.com/display/public/DOCS/Understanding+Marketo+Custom+Objects#UnderstandingMarketoCustomObjects-customcompanyUsingCustomObjectswithCompanies.
I hope this helps somewhat! My experience with Leads was that Marketo only let us link with certain fields as well (Salesforce ID I think in our case).
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