Firstly, while you disable SIP to use CAT, once in place you then re-enable it. SIP does not need to remain disabled for this to work.Hmm, I don't like to modify my OS, because I think you will be more vulnerable for malware.
Too bad that Apple tries to prevent this upgrade after Yosemite...
Secondly, if you have concerns about running a community provided tool, then don't use it. You can make the changes that CAT makes manually by following the instructions here:
https://github.com/dokterdok/Continuity-Activation-Tool/issues/397
From a security standpoint there is literally no reason not to do this. In fact I don't see a single reason not to do this. It adds great functionality with zero negatives.
The only reason Apple don't whitelist the Mac Pro as having this functionality is because it never shipped with a Wi-Fi/Bluetooth card capable of offering these features. The card was never considered to be an upgradeable part. Sure, it was an optional part in the 2009 model but they only ever offered one option. They did not intend for people to install 'sourced/modded' Apple cards from an iMac for example.
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