A slight mix up in terminologies here I think.
Bulletproof/Waterproof inks are what in UK are called Permanent inks meaning that they are much more resistant to being faded or washed out by exposure to water or caused to 'bleed' out by just too much moisture,these are rather water resistant than waterproof as against the 'washable' inks which in theory at least can be removed from clothing and paper by washing with water and for best results a detergent
The inks that should not be used in fountain pens are the 'Indian' inks and others containing shellac and other assorted chemicals which do the inner workings of fountain pens little good and in many cases stuff them completely and require at best a complete strip down and at worst complete replacement, these inksare designed for use with dip pens and with some stylographic these are the pens with needle and tube nibs, pens like Kooh-i-noor, rotring Isographs etc. There are also some acrylics based formulations designed for use with airbrushes and technical pens and the like that are in the vast majority of cases not for use in FPs and the old adage of in doubt don't is best followed.
Noodlers inks are like many modern inks highly saturated with pigments or dyes and particularly in the case or reds and purples can cause staining to certain plastics, although in most cases they are perfectly safe to use in modern fountain pens there are certain exceptions, if you have one of the exceptions then it is likely that you will want to avoid certain colours and will know about the potential problem, although if you rinse your pen through regularly there is usually little to worry about.
Then there is the situation where some pens have feeds and flow characteristics or the owners might have preferences about the flow characteristics of certain inks in certain pens but this is a purely personal thing.
I have rambled on a bit tut i hope that it has helped things and not muddied the waters and confused you more than you were before.