Attempt to use a blank (nulls just test sample) 64-byte stub:

4D5A0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000040000000

Attach it via format pe64 on 'stub.bin':

4D5A4000010000000400000000000000000000000000000040000000000000000000000000000000000000000000000000000000000000000000000040000000

FASM treats it as a legacy MZ executable (e_lfarlc < 0x40) and overwrites e_cblp, e_cp, e_cparhdr, and e_lfarlc.
How to attach a raw stub as-is without FASM modifying these fields?

Also tested with 0xFF fill:

4D5AFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF40000000

• FASM 1: error: value out of range. (or out of memory)
• FASM 2: (heavy lag) Error: error reading file 'stub.bin'.

In FASM 2 (pe.inc), e_cp = 0xFFFF calculates .TEMPLATE_LENGTH ≈ 32MB, and it tries to read 32MB from a 64-byte file. Can this file size check
be added or bypassed?

Some fields in the MZ header need to be correct for the loader to find the PE header. So modifying the header is needed for the file to load correctly. Without the changes the file is not valid.

To get a raw header with all zero bytes, manually overwrite the header after fasm creates the binary. The file probably won't run after that because the PE header offset is lost. Try it and see what Windows makes of it.