The wording "When the sequence of the content affects its meaning, that sequence can be programmatically determined" is ambiguous as to whether it refers to intended viewing/reading order, keyboard navigation order, presentation order (e.g. navigation links are at the top despite the designer's intention that they not be actually read on every page), and/or declaration order (e.g. content is declared early in the HTML despite being positioned at the bottom of the page using vertical alignment attributes). The Understanding section only addresses conveying intended reading order, but if that is the intention, the wording of the Success Criterion should reflect that. However, other ordering may be important to some types of assistive technology (e.g. keyboard navigation order for use by speech recognition software).
Yes, it is the intent that SC 1.3.2 (formerly 1.3.3) cover only reading order. Keyboard navigation order is covered under SC 2.4.3 (formerly 2.4.6). The other aspects of the comment - presentation order and declaration order are considered to be aspects of or sufficient techniques for the above two issues. To clarify this, SC 1.3.2 was reworded: "When the sequence in which content is presented affects its meaning, a correct reading sequence can be programmatically determined and sequential navigation of interactive components is consistent with that sequence."