I have not done a UAD 3.6 yet. However, the fundamentals of appraising remain the same. UAD is a format for reporting - it asks for more detailed data or more separation of data reported on the first page, which does not mean you have to adjust for each and every piece of data reported on the sales comparison approach.
A one-off repair issue, such as standing water in an otherwise good or average condition house, is different than a run-down, depreciated house where the standing water is only one of a set of items needing repair/replacement.
Usually, when a house is depreciated enough to need signficant repair and /or replacements, the buyer changes from an owner-occupant to a property flipper or investor ( who is willing to tackle run-down houses needing significant repair or upgrades, and expects a discount that allows for a profit ) In additional, the property flippers and investors are usually cash buyers vs the owner occupants who can be cash, or financing.
If the standing water is such that observed structural integrity is at risk, that is another element, and even if the value is AS IS, you can recommend an inspection and state that if the home damage because of the standing water was beyond what was observed, the appraisal results could be different.