It's difficult to provide an accurate solution without a visual representation of the project you're working on. It seems like you may need to think outside the box and find a creative workaround. If you can share the code, that would be really helpful.
You might be correct in assuming that a lower z-index could make an element unclickable, especially if there are transparent divs or margins/paddings blocking it.
Suggestions:
1. Check if you can use relative positioning instead of relying solely on margin and padding for layout. Keep top-level divs compact to avoid unnecessary obstructions.
2. Consider placing an invisible div over the element to mimic clicking on the hidden element (although this is considered a hack and not recommended practice, sometimes it's necessary for functionality).
These are just educated guesses without seeing your specific project. Sharing more details will allow for a more tailored and effective solution!