I'm looking for best practice recommendations for using one domain in 2 different marketing automation instances (for email and webpage activity). Does anyone have experience doing this or know if there are any complications related to doing this? Specifically, Marketo and Pardot are the two I'm working with.
There aren't any inherent complications, but you certainly can create complications if IT doesn't get that both instances are live (as opposed to one replacing the other).
For example, to the degree that you need to add Marketo to your SPF entry (that is to say, usually not at all) you'd need to make sure to include:mktomail.com as well as include:pardot.com or whatever (and you need top make sure you don't overflow SPF DNS lookup limits when doing so, which is why you shouldn't add Marketo's entry unless you actually need to).
The DKIM selectors won't overlap, so that's not a problem.
You can't use the exact same landing page domain for both MA platforms (which may be obvious), but marketopages.example.com and pardotpages.example.com can coexist just fine.