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It seems that the embedded abi can be used even in programs that use the full RV32I instruction set1. This flag only determines if the embedded abi is used as I understand it2, not if the object file is limited to RV32E instructions.
Footnotes
https://github.com/riscv-non-isa/riscv-eabi-spec/blob/master/EABI.adoc#1-goals ↩
https://github.com/riscv-non-isa/riscv-elf-psabi-doc/blob/master/riscv-elf.adoc#file-header ↩