I don't agree with you that Mana spells should only be able to be cast from the astral plane, that mana spells can only stun or that an astral caster should be allowed to affecting living targets on the physical plane that does not have an actual tangible presence on the astral plane.
But I do agree that indirect combat spells could be renamed physical combat spells (which mean they are affected by things like physical armor, physical barriers and line of fire) and direct combat spells could be renamed into mana combat spells (which mean they are affected by things like mage armor, mana barriers and line of sight).
Mana spells in no way shape or form should influence the Physical world. That is the whole point of having Mana vs. Physical spells.
I don't think I (nor the authors of Shadowrun) share your view on this....
If you want to cook someone on the physical plane from the inside out you use a mana spell that deal physical damage (mana barriers and mage armor helps against this). This used to be called a direct combat spell but I agree with your that this might as well just be called a mana combat spell.
If you want to cook someone on the physical plane from the outside in you use a physical spell that deal actual fire damage (physical barriers and physical armor helps against this). This used to be called an indirect combat spell but I agree with you that this might as well just be called a physical combat spell.
It was a mistake to ever let that be the case.
The reasoning here is that you need to target an actual form.
If you cast a spell on the physical plane then your target need to have an actual tangible physical form.
You can't target wholly astral entities from the physical plane.
If you cast a spell on the astral plane then your target need to have an actual tangible astral form.
You can't target intangible astral auras of living targets, only actual tangle astral forms from like dual natured or wholly astral entities.
What is cast in astral stays in astral.
This prevent spirits and projecting magicians from targeting physical guards on the physical realm without risk of being targeted back. Which is a Good Thing. If you want to hurt someone on the physical plane then you need to expose yourself on the physical plane.