A family of Microsoft word processing software products for creating web, email, and print documents.
When Style Sets were first introduced, was told (by MS) that, as you observed, the styles in the Style Gallery are those saved in the Style Set. One piece that I didn't see mentioned in this thread is the Document Defaults are also saved and when a Style Set is applied, the Document Defaults are also updated. This is the primary difference between using Style Sets and the Organizer. Actually, that may be the only difference.
Here's what happens: When you apply a new Style Set, all styles in the Style Set file with the attribute of tw:qFormat="1" in styles.xml along with the Document Defaults are "copied" to the destination document. (They aren't really copied, the style properties in the destination document are updated in the xml.) If a style isn't part of the Style Set, it remains untouched when a new Style Set is applied. With that in mind, any custom styles that aren't defined in the Style Set will not be updated and remain in the Styles Gallery, provided the style includes that attribute and if it's in-use in the document. It will, however, inherit formatting from the Document Defaults.
If there are discrepancies when applying a Style Set to other documents, it's likely due to the Theme that's in use in the destination document and whether the styles were formatted using theme elements, such as Heading and Body fonts, theme colors, etc. rather than absolute formatting.
Another discrepancy possibility is there is a conflict between the Normal style and the Document Defaults. This shouldn't happen, but I've encountered it a couple times. As with most Word features that pertain to formatting, it's recommended the Normal style remain an empty style (especially in Style Sets) in order to avoid the table style bug and other style hierarchy issues.
For those not familiar with how the Normal style works in Word 2007 and up, when the file format changed to xml in Word 2007, the Document Defaults were no longer hard-coded and could be modified. (Prior to Word 2007, they were hard-coded in every document as TNR, 10pts, single space, etc.) In all versions, the Normal style is empty by default. IOW, by default, there is no formatting defined for paragraphs or characters for the Normal style and all formatting is inherited from the Document Defaults.
Now that we can modify the Document Defaults, there's no reason to modify the Normal style and it should remain empty in order to avoid the issues previously described. The reason for those issues is due to order in which Word applies formatting: first it applies formats defined in the Document Defaults, then Table Styles, then Paragraph Styles, and then Character Styles. Since the Normal style is a Paragraph Style, when you're working with tables its formats are applied 3rd, which is why hierarchy issues could be encountered if it's not an empty style.