Dear Pepe,
I tried this out, but my experience is different. I have a similar situation: one of the equivalents for "holy" is "santus", and "Holy Spirit" is "Espritu Santus".
When I connect both terms to their respective glossary entry and link both terms, PT gives error messages:
MAT 1:18 "Unable to link Espritu Santus. It overlaps with Santus". In MAT 1:18, no \w ... \w* marks are added. The same happens in all places. There are just three exceptions, and these are cases where "santus" as such occurs earlier than "Espritu Santus" in a chapter. As I have linked only the first occurrence in the chapter, the 2nd occurrence of "santus" will not be marked, hence when that 2nd occurrence is part of Espritu Santus, Espritu Santus will be marked. This happens e.g. in HEB 9:8 (verse 2 has Santus). But everywhere where the two overlap, nothing is marked.