Appropriate skill checks don’t pop up when bringing up the 12-hour work day to Overseer Griggs in “Now Hiring: Invaluable Disposable Agent”. My engineering is maxed and I know this dialogue is supposed to have an engineering check, but no dialogue option is available.

I have the same issue. None of the possible checks actually show up in the conversation (locked or otherwise), but I tried putting 7 points into leadership and that actually made that option appear. Can't get the engineering one to show up at all, however.  

I cut a ticket to Obsidian and they said this:

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This conversation doesn't have any Engineering skill checks. There're some dialogue lines which requires Leadership skill [...]

There are screenshots online showing the Engineering check my guess is that they could have been unintentional and from an earlier build.