In the following Glossary entry for adaptation the primary and secondary stress indicators are used:
Pretty straight forward. The secondary stress indicator (less bold) is used and then the primary stress indicator (more bold).
In the Glossary entry for attract a secondary stress indicator is shown.
The question is this: since the only stress indicator is the secondary version, does it therefore become a primary stress indicator since it’s the only stress indicator used? Or is the secondary used as shown in print?
I agree with you. Treat each word independently. If it has only one stress mark, that is primary. Disregard what stress marks in other words may look like. When you have a word with the two stress marks, it is clear that one of them is primary and the other secondary.