The SS only became the powerful force rivaling the military and controlling parts of the party after the July 20th coup attempt, which won't happen in a Nazi victory scenario.
The Wehrmacht is still the sole uncontested fighting force, the Abwehr won't be absorbed by the SD and the Gauleiter enjoy a lot more independence.
I'm basing a lot of this off CalBear's AANW but wasn't it Hitler's goal even before 1944 to create and establish a Wehrmacht that was entirely Nazified with an indoctrinated/ideologically devoted Officer Corps, NCOs, and enlisted troops who were raised from the cradle in Nazi doctrine and graduated from the Hitler Youth?
If the Reich won the war the Wehrmacht would shrink greatly as a significant amount of soldiers would retire for good or return to civilian life and civilian work. A post war Wehrmacht wouldn't be as large as it was during the war. What's stopping Hitler from simply using this period to remove and retire those officers and generals who aren't politically reliable enough and aren't sufficiently devoted to National Socialism and replacing them with those who ARE fanatics and devoted to Hitler and the Party? Nothing really.
I don't see it as the Waffen SS replaces the Wehrmacht but as they merge together with the result being a completely Nazified from top to bottom armed force almost entirely full of troops and officers who may not be professionals in the Manstein/Guderian sense but are chosen for their beliefs and adherence to Nazi doctrine (racism, Social Darwinism, devotion to Hitler etc).
If after the war Hitler retires Manstein for example, what is Manstein feasibly going to do? He can try to subvert the Fuhrer's will or let it go and live the rest of his life in peaceful luxury off a pension in an estate in Poland. Would he really try to overthrow Hitler who in the public's mind has defeated the USSR and held the Jewish run Anglo Americans at bay and is responsible for the unprecedented conquest of Europe from France to the Urals simply because he doesn't have a job anymore?
Which would your average professional German officer do if given that choice?
How many officers and NCOs would seriously contemplate organising a coup against a victorious Reich with Hitler and the Nazi Party enjoying almost complete approval from the population?
Which is the more reasonable decision given the circumstances?
Remember the cost of a failed coup or a coup plot that gets uncovered. You're going to be tortured and brutally executed and your family is going to be sent to a concentration camp. If I had a choice between retirement and treason with a high likelihood of torture and death for myself and my loved ones, I'd take retirement and my pension and not make waves as it's pointless and unnecessarily risky.