Pardon me but to install custom roms you require a custom recovery which would trip Knox?
Okay, so first of all ask yourself whether you want to use knox specific features such as secure pay (Pay by using NFC), KNOX enterprise features which an average user will not use.
Secondly, If you wish to remove apps that are pre-installed on the device as they may be slowing down the device and ruining battery life then you will have to root or install a custom rom to deal with those, or you could simply try disabling them in the app manager without root.
After rooting if you use Touchwiz based custom roms you will still have 99% of the Note 4 features still available and sometimes you get additional features which would otherwise not be available for example removing restrictions such as recording calls which maybe disabled in your region or carrier. This is just one of the many features that you gain.
So your Spen, fingerprint scanner will all work as long as you use a Touchwiz based rom.
If however you want to use the latest and greatest version of Android and enjoy a clean and smooth experience then you may wish to install AOSP roms however they currently do no support fingerprint scanner and nor do they have built in SPen features.
A custom recovery will allow you to backup your current rom and restore it later if you so desire, this backup will store you settings, apps and the current rom which can be restored if you want to return to the setup.
The only con of rooting and flashing is that you read the instructions in the thread and do no deviated from it unless you know what you are doing.
Voiding your warranty is also a potential con, however here in the UK and Europe Samsung will have to repair your device in accordance to the law and I have had my Samsung Galaxy S4 repaired multiple times with the KNOx warranty tripped; however Samsung have rejected some claims in the past for some people.
If you have anymore questions then please do not hesitate to ask.