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.