If I worked abroad for a Canadian employer, do those days still count toward my citizenship physical presence?

Generally, no. The citizenship physical presence requirement counts days actually, physically present in Canada within the relevant period before applying, and working abroad, even for a Canadian employer, does not itself count as physical presence in Canada. This is different from some of the residency obligation exceptions that exist for permanent residents, where qualifying employment abroad for a Canadian business can sometimes count.

There are narrow, specific exceptions built into citizenship law for certain categories, such as being posted abroad as a Crown servant, but ordinary private employment abroad, even for a well-established Canadian company, is not treated as physical presence in Canada for citizenship purposes. This distinction between the permanent resident residency obligation and the citizenship physical presence requirement is a common source of confusion, since the two systems use different rules despite sounding similar.

Anyone planning significant time abroad for work while working toward the citizenship physical presence requirement should assume that time generally will not count, and plan the timing of their application accordingly, rather than relying on an assumption borrowed from the permanent resident residency obligation rules.