With Speed Unequalized, Relativistic Zs'Skayr speedblitzes The Flying Dutchman.
Also, due to Soul Manipulation, he can destroy The Flying Dutchman's soul, which is, obviously, all that the The Flying Dutchman is. Insta-deader-than-dead.
Also:
Regeneration (High over time;
Ben stated that even if Zs'Skayr has been shredded to atoms, he'll be back, and has done it multiple times)
I question how scientifically knowledgeable of an alien's biological capabilities are on an atomic level Ben Tennyson is, especially since he is often noted as not that book smart.
Still, if we're to take Ben's word as scientific fact, & Zs'Skayr has indeed, Regenerated from mere atoms, & can do so in a combat applicable timeframe, that's a problem.
With Speed Equalized, The Dutchman MAY have a chance, though.
BFR (Can send people into The Void, the Fly of Despair and Davy Jones' Locker.
His ship cannot be left by natural means, as people will instantly find themselves back in there, should they try to escape, and
the only way out is through a door that leads to a perfume department)
AFAIK, Zs'Skayr has no answer to being BFR'd. Is it in-character for The Flying Dutchman to do so immediately, as his first move?
Relatedly:
limited
Creation (Materialised a chest to put Patrick and Spongebob in, and then a bridge to take them onto his ship),
Soul Manipulation (Took the souls of Spongebob and his friends in
The Legends of Boo-kini Bottom)
Another possibility:
Illusion Creation (Created several illusions to terrify
Squidward in
Ghost Host)
Might be relevant; If Zs'Skayr doesn't know what he's dealing with or where his opponent is, he's less able to attack where his opponent is to one-shot them, as he would.
Electricity Manipulation,
Mind Manipulation (Turned Plankton into his minion with a single zap)
Zs'Skayr seems to lack Resistance to these. Mind Manip, GG?
Magic (Can grant wishes)
If offered a Wish, what might Zs'Skayr wish for in this context? What are some ways such wishes could be turned against him, as a would-be Jerk Genie like The Flying Dutchman might?
Also:
Teleportation (Used in
Shanghaied to block
SpongeBob and
Patrick from leaving his ship with his dining sock, and in
Born Again Krabs to transport himself and
Mr. Krabs to Davy Jones' Locker),
May be useful for avoiding Zs'Skayr's attacks, or maneuvering him into more favorable positions.
Fear Manipulation
Zs'Skayr has, funnily enough, no resistance to it, & your opponent being paralyzed (As in, inactive.) is pretty good when you have several ways to quickly win against them.
So, uhhh, yeah. Equalize speed, & The Flying Dutchman appears to have SEVERAL win conditions, many of which Zs'Skayr lacks an answer or Resistance to..