bag of visual words -Difference between default and custom extractor

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What is the difference between DEFAULT and CUSTOM EXTRACTOR?
DEFAULT: No need to define, just one line in program:
bag=bagOfFeatures(imageset1A);
Information: I used default (should be SURF) and program extracted 2439360 features from first category. I used custom extractor (detect and extract SURF)and program extracted 16649 (64 dimensional) and 16352 (128 dimensional)features from first category.
Problem: Why this difference? Also execution time is around 1 hr for default whereas 5 minutes for custom extractor.
accuracy with default is better than with custom extractor. I am not using any customized parameters in custom extractor. See below:
Content of custom extractor (Myextractor):
InterestPoints = detectSURFFeatures(grayImage);
features = extractFeatures(grayImage, InterestPoints);
Content of program:
bag=bagOfFeatures(imageset1A,'CustomExtractor', Myextractor);

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