Warren Worthington the III was a child 10 years before X-Men the Last Stand but a late teen to early 20 something in X-Men Apocalypse set in 1983. Jean is a child 20 years before TLS film events again this doesn't mesh with the X-Men Apocalypse version of Jean which is a teen by 1983. Moira is a geneticist and played by an actress born in 1968 in The Last Stand but is an CIA Agent active in 1962. So Cyclops' age means nothing.
As for Stryker not knowing Wolverine well Xavier forgot Mystique was his sister in the 1st 3 X-Men films. We must assume for some reason he chose to ignore it like Stryker ignored knowing Wolverine.
Also there is no mention that Wolverine and Creed missions pre Stryker were black ops that's just something you're pulling from your own head canon to try and make it work.