Aside from a few outliers, when speaking about Strengthening of a magus' own body, practically speaking that means the enhancing of muscle strength and agility, but that doesn't necessarily include an improved stamina. Rather, since physically exerting oneself while performing magecraft exhausts both physical and mental energy, one could say it would more likely have a negative effect.
Of course, that all depends on the skills and talent of the caster, and there were plenty enough examples of those who were talented enough in Strengthening to be able to perform with little to no impact on their overall stamina.
Case Files III, Chapter 2, Part 3