Once a "custom verse" is accepted by Paratext because of the custom.vrs, it will be treated like any other "standard verse", like adding footnotes to them.
I understand your question is whether you can have an empty verse containing a footnote and the answer is yes. In this case the callout will be placed next to the verse number. When you enter biblical text in it you must be careful under which word to leave the callout.
As an example, you can see in the image I have added the verse MAT 18:36, which has no text but has a footnote and does not give a verification error:
If it's not working for you, could you share a little more information about where it's sending you the error messages?