Discovery can't get a transporter lock on Tilly because she's in a room with Tritanium walls and the windows have all shut. At that point, the openings in the ceiling were unblocked. It was only later that the overhead openings were closed. Discovery should have been able to get a transporter lock prior to them closing.
The Discovery crew reason that Dr. Kreel disguised the weather control/force field device as a mountain to avoid contaminating the planet with advanced technology and thus adhere to the Prime Directive. The Prime Directive is noninterference with the development of a pre-warp civilization. Installing a weather control device/force field generator wildly disturbs the planet's natural development, regardless of what it looks like.