Making a controller - Do I need to take the low pass filter into account?

I really have no idea what you're asking [????], and your link didn't seem to work,
but after some massaging I got to here, which shows a different transfer
function:

http://sim.okawa-denshi.jp/en/PWMtool.php

However, the other link above the text on that page is much more straightforward,
and is the formula I've used for many years to compute 1st-order 3dB rolloff
frequency:

http://sim.okawa-denshi.jp/en/CRlowkeisan.htm

F3dB = 1 / (2 * PI * R * C)

Basically this is a simple low-pass filter that smooths out the PWM signal to give
a DC voltage with some small ripple riding on top.

Is your motor controller supposed to be taking a DC voltage input? Most motor
controllers, it seems to me, actually use the PWM directly. ????