The two email sends are in the callback.aspx.vb file in the root of the site. There are comment blocks that headline both the mail send to customer, and to store admin.
Whether HTML is used or not should depend on the same boolean value for both (at least in the latest file I can see which is checked into codeplex);
SendEmail(strFromEmail, UsersBLL.GetEmailByID(O_CustomerID), GetGlobalResourceObject("Email", "Config_Subjectline") & " (#" & O_ID & ")", strCustomerEmailText, , , , , blnUseHTMLOrderEmail)
And the store owner email:
SendEmail(strFromEmail, LanguagesBLL.GetEmailTo(1), GetGlobalResourceObject("Email", "Config_Subjectline2") & " (#" & O_ID & ")", strStoreEmailText, , , , , blnUseHTMLOrderEmail)
(note the true/false value 'blnUseHTMLOrderEmail')
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