I am aware that the Squadron Engineering and Survival Manuals overwrite FC buffs, but I cannot find any information if the experience buff from Commercial and Company-Issued Manuals will still apply while a Squadron Manual is active?

Since Squadron Manuals act as personal FC buffs and the Commercial/Company Manuals stack with FC, I am lead to believe that Squadron Manuals do, indeed, stack with Commercial/Company Manuals.

(Commercial/Company Manuals grant you the buff "Crafter's/Gatherer's Grace", not aware of the name of the buff granted by Squadron Manuals.)