There are a few stores (like Target) that are now offering a debit card which is tied to your account at a bank. The transactions post to the account as an ACH item, but specifies in the description that it is the Target debit card POS transaction. Since it is not a POS transaction to me, do the overdraft rules apply as far as charging NSF fees?

You do not need to worry about customer opt-in opt-outs and charging fees. If you are presented with an ACH debit for a decoupled debit card, you are free to charge a fee, pay the item, return the item, etc. regarding of the opt-in status oof the account.

You'll find the "carve-out" for decoupled cards in Comment 17(b)-1.i.:

1. Scope. i. Account-holding institutions. Section 1005.17(b) applies to ATM and one-time debit card transactions made with a debit card issued by or on behalf of the account-holding institution. Section 1005.17(b) does not apply to ATM and one-time debit card transactions made with a debit card issued by or through a third party unless the debit card is issued on behalf of the account-holding institution.