I know that under 229.13(e), reasonable cause to doubt collectibility, the commentary says you cannot doubt collectibility on a category of checks. But, under the large check extended hold period, can we implement that hold for only insurance checks over that amount or do we have to implement the extended hold for ALL checks over that amount?

Targeting a specific type of check, regardless of the type of hold utilized, is not permitted.

My recommendation is and always has been to use a risk based approach. I instruct front line staff to ask themselves:
1) How likely is the item to be returned?
2) If it is returned are there normally compensating balances available for charge back?
If not, place the hold---if so, just deposit it.