Text Book Answer: Matched Paired Analysis. Find two homes that are identical with only one exception, size. We found these in new tract home subdivisions. Same builder, homes next to each other, 3bd 2ba with fireplace and 2 car. Home A sells on Monday, Home B sells on Tuesday. One is 1300 sf and the other is 1420, etc. We were able to determine a "market derived" cost per square foot differential. In a perfect world we would do this on every home across all of the quality levels. Yeh, yeh, yeh. What we realistically had to do was define that as our market derived psf $ amount and adjust upward or downward from there. Manufactured homes might use $20 in stead of $25 for above grade. "Good" or "Very Good" might use $30 or $40 instead of $25 for example. Walkout basements would only be a percentage of the above grade. Its all relative. The more unique your subject (Excellent Quality) the less accurate this becomes. The bottom line is let the market tell you. Look at your three comps, what do they tell you? I love to see condo appraisals because they are the easiest to do a matched paired analysis on.
With respect to your question about the 100 sf, I concur with previous comment. We adjust them all in our office. If the 100 sf is on a 5000 sf home, this dollar amount should only be small (%) anyways and should not be a concern with Gross and Net adjustments. If the home is 700 sf then the adjustment should be relatively larger.
Keep asking questions, after 10+ years I still do. Every situation is different so don't always try to put the square peg in the round hole. Step back and try to figure out what seems reasonable.