It's not beig used as "type" or "method" here though.

"course of antibioctics" - course refers to the time frame, hte starting and completion of taking drugs. It is not to do with which type.

"course of treament" - here we run into two meanings.
One can be "method, type"

"Chemotherapy was the course of treatment chosen".

This is NOT the same as:

"A course of Chemotherapy was chosen"

Because it is acceptable to say (although the repetition of Course makes it sound a bit clumsy)

"A course of Chemotherapy was the chosen course of treament".

Here the first Course = plan, schedule, regime.
The second Course = route, method, type.

"A Chemotherapy regime was route chosen"

Meh. I understand what I mean anyway.