Yes, taking the barrel on/off will effect the POI of the optic...but not too much. You may not even notice it. Especially if you are using a red dot that already has a 2MOA (or larger) reticle.
If you were using the rifle to see how small of a group you could shoot at 100M, and removing the barrel from the receiver when you stored the gun, that definitely not ideal.
But, if you are just plinking or having fun, you will never notice the difference.
There isn't enough space to mount anything else but one optic...the mount is only about 1" long...maybe 1.5". I don't foresee any alignment issue if you mounted the red dot on the forward rail and a magnifier on the receiver...the barrel/receiver alignment may change .5mm either direction, but that is very negligible for that combo.