I went through the SURGE rules and found that the surge based qualities do not count against the BP for class III. I wanted to ask if this was indeed the case and that the chargen.php page is slightly buggy, or if it was house ruled that they do indeed count against the initial BP. Right now I'm working out a concept character but until I know what is the real story, I can't go too much further.

Reasoning:
If you look at the beginning of the SURGE positive qualities, it'll state the following: Depending upon the Class of SURGE picked when buying the Changeling quality (p. 73), the character gains a number of Positive BPs that may be spent on the Metagenics qualities below as well as those listed above.

The same deal happens for negative SURGE BP's.

Class III says you are required to pick a theme for the SURGE, and secondly that you have to pick at least 30 BP of positive surge qualities and 15 of negative, of which some that are not specifically listed as surge qualities can also be included.

(pg. 110, RC) The stuff that can also be bought with SURGE:
Other Positive Qualities: Astral Sight, Biocompatibility, Double Jointed, High Pain Tolerance, Magic Resistance, Natural Hardening, Natural Immunity, Quick Healer, Resistance to Pathogens/Toxins, Spell/Spirit Knack, Toughness

Other Negative Qualities: Allergy, Asthma, Albinism, Biosystem Overstress, Disease Carrier, Gene Freak, Low Pain Tolerance, Nano Intolerance, Reduced (Sense), Sensitive System, Uncontrolled Metastasis, Weak Immune System

There are no house rules here.

And there are many odd issues with Chargen. It does not figure BPs for you, nor does it penalize you for going over BP. We leave it to the honor system (and the Hangman, which doesn't seem to be working at the moment) to keep people from abusing the system.

Yep, the chargen is do-it-yourself for calculating your BP correctly.  And you are indeed correct about how Changeling works.

The way I've done all my SURGEd characters is as follows:

Just add the positive qualities on and the negatives.  If you take your 30 points of SURGE positives, and 15 negatives, you've spent the 15 BP of the SURGE III quality, for instance.  Done.

Yeah, at the top of CG it states: "May Not Include Foci or BP-Adjusting Qualities"

The workaround from NES sounds good. Another option is to adjust the BP by using the override field in CG.