I've been trying to get the Atomic artillery shell auto-targeting to be a bit smarter, sometimes it seems to place shells a good distance apart, sometimes it shoots two shells at the same place (vanilla bug maybe?).
I saw this thread in the standalone atomic artillery shell mod discussion: https://mods.factorio.com/mod/AtomicArtillery/discussion/5f7554729685683497246bb2
I've tested the order of the projectile radius effects, and haven't found a difference between how it currently is, and moving the effect with radius = 35
to the top as suggested in that thread, the order doesn't seem to have any effect. Also, testing with that mod (which has the "fix" applied) doesn't seem to have better auto-targeting.
Your observation is correct. The issue comes from the vanilla game.
The artillery shell auto-targeting algorithm is hard-coded and is unknown to (most, if not all) modders. There is no way to set "proper" radius to various artillery shells in mods. So the issue happens not only to your above-mentioned mod or this mod; but global to any mods that want to do anything about artillery shells.
Regarding this, is it possible you could implement something like this mod: https://mods.factorio.com/mod/AtomicArtilleryRemote
It creates different artillery cannons for the atomic shells, so you can have a targeting remote for your atomic shells. Maybe have it as an option in startup options?
I would be happy to adapt that mod to a new one and upload it myself, but it would be better if it's supported from the base mod.
The mod you mentioned is duplicating a lot of prototypes (including artillery turret item+entity+recipe, artillery wagon item+entity+recipe, artillery flare, etc) in order to achieve such separate targeting. This may look fine if you have only the vanilla artillery shell and one atomic artillery shell.
However, this approach would require an extra set of all these prototypes for EACH type of artillery shell. Considering this mod is offering four types of new artillery shells, such approach will make the game really cumbersome. (Think of five types of artillery turrets, five types of artillery wagons...)
Therefore, this is not an elegant solution to overcome the vanilla issue, at least not with this mod.