You're right that §208A(e)(1) mandates that only expenses attributable to rental at fair market value may be deductible where "the taxpayer...uses a dwelling unit for personal purposes on any day during the taxable year (whether or not he is treated under this section as using such unit as a residence)".  In other words, depreciation allowance must still be allocated between rental and personal use even though the taxpayer used the property for less than the thresholds defined under subsection (d)(1) and the deductions would not be subject to the subsection limitation under subsection (c)(5).

PTO does optimize the allocation of mortgage interest and real estate taxes between Sch A and Sch E so long as the number of days owned is entered.  However, I do see two technical problems in PTO's computation when the taxpayer did not use the property for more than the greater of 14 days or 10% of the days rented at FMV (i.e. when the property does not qualify as a residence/vacation home) -

1. Mortgage Interest: PTO allocates mortgage interest to Sch A even though the property does not qualify as a residence and the interest paid would not constitute deductible qualified residence interest as defined under §163(h)(4)(A);
2. Depreciation: PTO does not prorate for rental use but allows full depreciation allowance.  As explained above, there is no technical basis for taking this position.