The root issue here is the lack of understanding of different airspace types and how they work. The confusion around 107.41 comes from lack of understanding about the layering of airspace (upside-down wedding cakes). Part 107 allows sUAS to operate in Class G airspace without the need for ATC approval. This is a large area, even around a big city. Class G airspace sits below Class E airspace, with Class G airspace typically defined as ground up to either 700' AGL OR 1,200' AGL. Either way, this is well above the typical sUAS operational ceiling of 400' AGL. Here is a great info piece on airspace types:
Airspace
I highly recommend purchasing a VFR sectional chart to study, especially the printed key. The shaded magenta area around an airport means that the ceiling of the Class G airspace (sUAS operational airspace) reduces from 1,200' AGL down to 700' AGL (still a 300' buffer for sUAS operations below the Class E airspace).
I am using the Cincinnati sectional chart for the following examples.
Look at KOXD: with Part 107 you can fly inside the shaded magenta circle, all the way up to the field (but not over) without getting ATC approval, because you are still in Class G airspace (under a 700' AGL Class E Airspace). (Would still need to follow 107.43 operation near/around airports and air traffic.)
Look at KCVG: the only space that requires ATC approval is the innermost solid blue ring right over the airport, because Class B airspace there is surface to 10,000'. If you go straight north from KCVG, the next space due north of the field is only Class B airspace from 2,100' to 10,000', which means under that is Class G airspace from surface to 700' AGL.
Look at KLUK: The only controlled Class D airspace that would require ATC approval to fly would be inside the blue dashed circle (controlled surface to 3,000').
Look at KILN: Here is an example of the Class E airspace referenced in 107.41 that would require ATC approval. The controlled airspace around this airport is the dashed magenta box (Class E from surface up to 18,000' MSL) and the blue dashed circle (Class D airspace from surface to 3,600').
Look at KDAY: Controlled Class C airspace requiring ATC approval is the innermost solid magenta ring (Class C surface to 5,000'), with the ring outside that only being Class C airspace from 2,400' to 5,000', and Class E from 700' AGL and up (leaving sUAS flyable Class G airspace under that; surface to 700' AGL).
RECAP: The only airspace requiring ATC approval for 107.41 sUAS operations would be innermost solid blue ring at KCVG (Class B), innermost solid magenta ring around KDAY (Class C), dashed blue line around KLUK (Class D), and both the dashed magenta box (Class E) and dashed blue ring (Class D) around KILN.
Hope this helps with some of the confusion. I am a pilot and have also confirmed this with an FAA rep at the local FSDO.