You've read it correctly on the conflict clause. The tenancy addendum is part of the lease, and where your lease says something inconsistent with it, the addendum governs. Your lease keeps everything the addendum doesn't touch.
The clauses most often affected are the ones about money and about ending the tenancy. The addendum prohibits you from collecting any rent above the approved contract rent, so a side charge to the tenant for the gap between contract rent and market is out. Charges for things the tenant genuinely requested, like a specific appliance, are handled differently and need the authority's blessing on how they're documented. Utility responsibility has to match what was approved, because the utility allowance was calculated from it, so you can't shift a utility onto the tenant mid-lease on your own. Late fees are usually allowed on the tenant's own share only, and some authorities restrict them further. Termination grounds are narrowed compared with what a market lease might give you, and you still have to go through your state's ordinary eviction process, which the addendum doesn't replace.
That's the general mechanism. How each of those interacts with your particular state's lease law is a question for an attorney in that state, and it's cheaper to ask before you sign than after.
On abatement: yes, if the unit fails an inspection and isn't corrected within the time allowed, the authority can stop making payments while the tenant remains. The subsidy stops, the tenancy continues, and the tenant is not responsible for the withheld portion. Payments generally resume once the unit passes, though usually without back pay for the abated period. That's the reason experienced owners treat inspection items as urgent rather than as a to-do list.