1) The basic idea is that it is more difficult to imbed bladerunes in items of lesser quality.
2) Accordingly, non-magical items or items with no bonuses cannot receive bladerunes at all. (i.e. you cannot put them on any given).
3) This is actually a second chance at failure (i.e. failing while casting the spell being the first), so it does not need to be identical to other chances of failure.
4) The way that it is setup, only exceptional weapons can receive bladerunes.
5) RM uses open-ended rolls as a standard, unless it says otherwise. While the "Basic Principles" do not specify, I would presume that the roll is open-ended, and thus, there is actually a chance to roll outside the given percentage chance.
6) Conversely, you could always rule that there is always a 1% chance of failure, regardless of the total percentage.
7) Remember also, those Basic Principles are basically defining the principles that the author used in writing the spell list. If you disagree with those principles, then as GM you can change them to match your vision. (for example, I have never used that percentage chance - we always allowed the bladerunes to be imbedded on any weapon that the caster wanted.
