PWM hardware control

[86 5.0L]

I have a MCP352X and have a few pwm fans on the way. one issue thats been bugging me is that upon bootup my pump will run 100% until i log in to windows and have either speedfan or the mobo software load up and control the pump. with the high speed pwm fans coming I was wondering if theres any hardware solution to this? like a pwm fan controller, i know of the diy option, and of the aquaero controller(dont know if this has 'instant' control or it needs to boot up before controlling a pwm device). Am i crazy for finding this annoying?