I've asked this question in the past, and as I recall the answer was something like "well, that's just the way it is" or "why does it matter" or something to that effect.
Let's just take a simple example. I use some of the canned reports and also some reports I have created to calculate income for tax purposes. To simplify this, let's say I have just one account, an Rollover IRA, and it is identified in the Account Details as Tax deferred. Under Tax Schedule Information, Transfers from this account are shown as "1099-R: Total IRA Taxable Distribution".
For practical reasons, I would want to show the distributions as income, but I don't want the interest or dividend income for that account's holdings to show as current income. Those interest and dividend income transactions aren't taxable until they become part of a distribution. But all the reports, regardless of canned or custom, show them as income because of their categorization as IntInc or DivInc. It doesn't matter if the account is tax-deferred or not. There are other categories that could be used, like DivIncTaxFree or IntIncTaxFree, but I suppose they are used for other purposes, and anyway, the user interface for entering transactions for the Investment type accounts don't tag them that way.
I see no way to separate out those transactions so that they don't get shown in the report as current income. Of course, I could just take all the IRA accounts out of the reports and handle them separately, but why?
The only other strange thing is that two of my IRAs show as Traditional IRA account type and the other one is just IRA, but not traditional. But in the drop-down list, "IRA" is no longer an option. Just Traditional, Roth, Keogh, SEP or Simple IRA.