My second home property taxes are listed on the 1098, however those taxes are paid to another state, and turbo tax combines them into my primary state's real estate taxes

Those real estate taxes paid in another state are still deductible in your home state.

It is correct on the return.

Somewhat like this concept:  If you made some money in another state, your residence state does not care where the money was made it.  It is still taxed by the resident state.  

Your resident state you report all income and all expenses to.  Then if it is income in another state and that state has income taxes, they will tax it also, and you get a credit for taxes paid to another state. 

Post a comment if this does not fully answer your question.  Thank you.