Absolutely a red flag. This is you stating your boundaries and then being punished for them. This is bullying and not domination, try explaining this and if things don't change leave.

Possibly as a result of your martial arts training. The idea that being punched was bad was drilled into you during that training and will still be there in your brain today

Then there's no cause for discomfort, well at least not metaphorical discomfort

Ok, rant out of the way onto the OP and technical stuff
How does one go about this fetish safely...
Practice, training, control and knowledge. I use punches (with varying degrees of clenching of the fit to change the impact) to achieve a more thuddy impact on buttocks. Sometimes even using kicks or Read more… elbow and forearm strikes. All delivered with a fairly precise amount of force. I've even used a re-enactment axe and sword on people before now, secure in the knowledge that I can pull the blow enough to avoid any real harm.
Why do some dominants enjoy obliging....
Well if you don't enjoy obliging your subs desires then you are looking at being on the wrong side of the dom/bully line. A dom should be all about bringing the sub what they want and need, not just doing what they want to a sub regardless.
Why are some submissives aroused by this...
Same reason some are aroused by being pissed or farted on or wrapped in clingfilm and left in the corner while you watch tv. They just are, it's their kink and that's fine

"Is Pirate being aggressive when he whips me?"
If there is any level of aggression in there then I would start to feel uncomfortable. Actual aggression has no part in a scene in my opinion, it is why I will never play when angry. A scene, especially a beating scene as discussed in the OP, must be Read more… controlled and done from a position of care. Never aggression.
This could of course be me getting on my high horse over terminology, for some people the terms aggression and violence can be interchangeable but for me aggression is always about the intent to harm. I will often intend to hurt but never intend to harm

Try calling "Red" on the ongoing orgasm denial...
If he won't respect your safeword and the fact that things can change based on behaviour then this would be a bit of a red flag.
Definitely time to talk about this and let him know the negative effect that it is happening on both you and your Read more… relationship, more importantly talk about how this has affected your perceptions of him.
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You are a proper submissive, a proper dom is aware that what they are doing they are doing for their submissive not just to them.
Anyone dom who tries to tell you that you are not a proper sub for having problems with things is not a dom, they are a bully