Jason,
I'm not sure what you mean by theoretically perfect. Just because a telescope is stated as diffraction limited doesn't mean its perfect. If we take a holistic approach, diffraction limited simply means the telescope has the ability to provide an Airy Disc. Diffraction limited optics are not particularly difficult to achieve from a manufacturing perspective.
A statement by a manufacturer indicating their optics are diffraction limited indicates that the optics are at least 1/4 wave peak to valley at the wavefront for a visible wavelength (usually 550mm yellow-green) as tested by an interferometer. A 1/4 wave peak to valley also translates to other optical calculations/formulas such as 1/27 wave RMS or an 0.80 Strehl ratio. I can provide formulas to calculate between these values if desired. So, these figures defined above are the baseline for diffraction limited optics. If the wave peak is not 1/4 wave (say 1/2) or the Strehl ratio is 0.60, the optics are not considered diffraction limited.
To answer your question, why pay for custom optics if production scopes meet the diffraction limited specification... Simply because diffraction limited doesn't indicate theoretical perfection (as previously mentioned). Theoretical perfection are optics that interferometer test at Strehl ratios of 0.97 or higher. To achieve this level of perfection takes considerable time and effort, something not viable in "run of the mill" high volume production line telescopes. If you want a higher optical quality than the basic diffraction limited specification, then you'll pay more for it.
Why would you want to pay for optics that are higher than the diffraction limited specification depends on your goals. Peter Ward has a great example of optical quality between an SCT (84% Strehl ratio that meets the diffraction limited baseline of 80%+) and RC (99% Strehl ratio) -
http://www.atscope.com.au/rcos.html
As they say, a picture speaks a thousand words.