Yes, we normally advise you against changing numbers on forms or changing forms in other ways. However, it is hardly possible to code for all the possible eventualities that you might find in doing taxes - especially since the law changes every year.
That is why we have to occasionally advise you to do workarounds so that the result is tax return that is as accurate as possible.
dmertz has correctly told you (both) that the way to get TurboTax to do what you want is to create two 1099-R forms, with the one having the 5% distribution in box 1 for the Roth IRA and the second would have the 95% of the distribution to the traditional IRA.
Then, for each 1099-R you can answer the questions in each case to apply to all the money in that particular 1099-R. This should solve your state issues as well.
As David said, the IRS looks at the totality, and besides, if they ever write you a letter wondering about this, you will have already documented what you did and why...you will, won't you? Just write this up for yourself and keep it in your tax files in case anyone ever wonders.
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