It's certainly a good idea to rate fuses a little lower than the wires, and you should consider wires in bundles as having lower capacity. However, wire rating it based on how hot the wires get, and they have much larger thermal capacity than fuses, so the short term rating is taken care of. 5 seconds at twice the rated current isn't likely to do any harm.
Also, just because the fuse is rated to blow in less than 5 seconds at twice the current, doesn't mean that twice the current is a likely fault. The likely fault current depends on all sorts of things.
If the current is larger, the fuse blows much faster, so the risk of wiring damage is much less. In fact the most worrying figure is up to 10 minutes at 135% of rating, as that is long enough to get considerable heat into the cable. I would aim for the cable to be rated 1.25 to 1.5 times the fuse.
Bundling is a separate matter. The rating there depends on the size of the bundle, and how many cables are going to be taking significant current. In a car, you won't get many cables taking much current at one time. The IEE wiring regulations have a lot of information about derating for bundles.