Hello Monte,
It seems that the section of m_cfmprotrom is generate by default , and it can not control through PE.
While you can do like this : configure the linker file by manually , then uncheck the "Generate linker file" :

then the linker file will not changed by the PE, and you can configure the linker file according to your peresonal willingness.
Hope it helps
.
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Have a great day,
Alice