As can be seen by inserting a flat in the Main Mirror's Light cone, the Main Mirror's Light Gathering Power is reduced by the shadow of the Flat.  The mirror's Clear Aperture is the difference between its Full Diameter and the total Diameter of the flat and its holder.   A 10" Main Mirror with a 1 7/8" Flat in a 2" holder will behave like an unobstructed 8" Main Mirror.
The size of the Flat also determines the length of the light cone's Tail, and therefore the distance the Prime Focus will extend beyond the side of the telescope.  The smaller the Flat, the larger the Clear Aperture, and the smaller the Tail. A larger Clear Aperture is welcome, but the Prime Focus must be kept within the Focuser's range.