The glazing units will almost always fail, at some stage (unless the never get exposure to sunlight).
With the butyl, if you are really careful, you can remove the glazing units and keep the seal intact. I've managed that many, many, times. Even if it does split slightly, it's seldom an issue.
If replacing the double glazing units, if the units are above a living space, especially in a bedroom, always fit toughened glass. If the units were to catastrophically fail, you wouldn't want shards of glass falling on family members. Generally, I tended to fit toughened on both units.
If the Velux unit is a single one without a similar nearby, fit a Low E pane as the inside pane as it reduces solar gain in summer and keeps energy in during the winter.
Velux panes tend to have a customised thickness of space bar (normally an odd rather than an even sized). You can round up to the nearest even sized mm (so 9mm would become 10mm, as an example). The glass units tend to be 4mm thick as the panes are seldom large enough to require 6mm thick glass.
While you can buy a full replacement kit from Velux for glass changes - with care, you can specify what is needed yourself and save a lot of money.