TurboTax definitely takes into consideration the $5K limit for State and Local Taxes for those filing Married Filing Separately. You are confusing mortgage interest and property tax. The HR link you included above only refers to mortgage interest. Mortgage interest is not a state or local tax, so it is not included as part of the $5K limit for state and local taxes for MFS filing status. Property tax or Real Estate taxes are part of that category. See the comparison here in this FAQ.
The IRS does not ignore the distinction between property taxes and mortgage interest. TurboTax takes into account all of the federal tax laws in the software including special circumstances. But it does not appear you have a special circumstance. If you are married filing separately, your property taxes (along with other state and local taxes) are limited to $5K. Mortgage interest is not a state or local tax, so this rule does not apply to mortgage interest. Mortgage interest can be limited, but by a different set of rules, see Can I deduct my mortgage?
You cannot override any numbers or calculations in TurboTax Online. You can using the desktop software. But keep in mind, if you switch to the desktop software and you do override numbers, you won't be able to e-file and any accuracy guarantees will become void.
**Say "Thanks" by clicking the thumb icon in a post
**Mark the post that answers your question by clicking on "Mark as Best Answer"
