1) I have Pulpit commentary opened to 2 Tim 4:2 but right click the reference 1 Tim 2:7 (below) and then select Add a note to ... . Unexpectedly a Note entry is created for 2 Tim 4:2, which is treated as a reference to my default bible. But if I choose Add to Passage List ... 1 Tim 2:7 is added as expected.
Further, if I right click a word in ver.2 (eg. "Teaching") and select the bible Reference a Note entry for 2 Tim 4:2 will be created, which is also a reference to my default bible (this is expected!).

2) DBL Greek is opened to ἀκαίρως GGK #178 but I select 2 Tim 4:2 (below) and then select Add a note to ... a Note entry is unexpectedly created for DBL Greek 178. But if I choose Add to Passage List ... 2 Tim 4:2 is added
as expected.
However, if I select the Reference Strong's Greek #171 I will get a Note entry for Strong's Greek #171 (as expected!).

The results in a Note file from selecting different data type References in a resource are inconsistent i.e. it will be a reference to the data type or treated as a Selection and reference the data type within the resource.