In the case of someone with an active weapon focus swinging at a manifested magician (which is visible to all, no Astral Perception required) I would say it would be Agility + Weapon Skill + Focus [Accuracy] vs. Intuition + Logic and damage would be Strength + Weapon + Net Hits to the manifested magician.
If an active weapon focus can hurt entities on the astral plane without the wielder being active on the Astral Plane (as you suggest) then you must also accept that wholly astral beings can hurt the owner of an active weapon focus out on the physical plane. This actually used to be a thing in earlier editions (you could for example ground an AoE spell from the astral plane through an active weapon focus to hurt it's owner on the Physical plane). This is not how it works in SR5.
While your idea might sound reasonable it would have to be considered a house rule. RAW on this matter is clear IMO.
"When you astral project you become a purely astral form... Manifesting is a psychic effect... manifesting doesn't give you a physical form... It's a psychic connection... You're still on the astral plane..."
(you have an Astral Form, unlike Materialization, Manifestation does
not give you a Physical Form)
"Astrally perceiving and dual-natured characters use their physical combat and physical attributes to attack opponents that have a physical form."
(for example a spirit that use the materialization power, but not a magician that use manifestation).
"Astrally perceiving and dual-natured characters use their ... Astral Combat + Willpower to fight wholly astral entities."
(for example a spirit that is not using the materialization power or a projecting magician no matter if he use manifestation or not).
By RAW a character on the Physical Plane cannot attack an Astral Form that doesn't have a Physical Form unless the character have a way of perceiving (dipping his head) or projecting (taking the full dive) into the Astral Plane, and in that case he would use Astral Combat and Mental Attributes. By RAW you are never allowed to use Physical Combat and Physical Attributes to attack an Astral Entity that doesn't have a Physical Form.