From reading this article, it seems extremely hard to "separate" the pre-tax and the Roth parts of 401(k)s -- you must always move them together. But moving them together is often not efficient; e.g. rolling them both over to a Traditional IRA will give you basis for the basis from the Roth, but basis in a Traditional IRA is not very efficient since its earnings are taxable; rolling them both over to a Roth IRA will cause conversion tax on the pre-tax part, which you may not want.
On the other hand, if you just had one or the other, it would be easy to deal with -- a completely pre-tax 401(k) can be rolled over to a Traditional IRA without any loss of efficiency; a completely Roth 401(k) can be rolled over to a Roth IRA without any tax.
Given this, is it a bad idea to have both pre-tax and Roth contributions in a 401(k)?