I agree that two Wittelsbach branches of different denominations would count at least as one and a half families ;-)
The lacking extra half comes from the fact that religion can still change (look at Palatinate-Neuburg), and that there might be still inheritance rights across these borders.
Wasn't the Bohemian crown still elective? I think in this tense situation it would take a war for the Habsburgs to dictate a king to the Bohemians..
Agreed. The Bohemian Diet would probably make some noise about the other Habsburg branch trying to depose their king.
You're right in that it wouldn't be so easy for the Emperor just to make the succession sure beforehand. Bohemia was electoral; de facto, that meant that the Diet of States had a veto against the Emperor's candidate (often the Emperor himself).
It rarely happened that a candidate was denied; the Bohemians even accepted, i.e. elected Ferdinand in 1617 who suppressed their long-standing privileges ... but of course, that's still some way down the road.