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Why are byte ports "ports" as such?

If you separate byte ports from character ports, and separate input ports from output ports (at least at the API level), you get an easily type-checked interface. e.g.

open-input-file string [encoding keywords] -> input-character-port
read-char input-char-port -> character
open-input-file-raw string -> input-byte-port
read-byte input-byte-port -> integer

For your bidi ports, perhaps

open-input-output-file string [encoding keywords] -> input-char-port output-char-port

with the two ports sharing common buffer structure in the implementation.

Often one needs to open a file or a structure initially as a byte port, then decode subsequent sections of the sequence as characters of a particular encoding. For that, a procedure like

cook-input-encoding integer input-byte-port [encoding keywords] -> input-char-port

can return a port that promises to decode a certain number of octets from the backing byte port with your encoding. It does't handle variable-length structures well, though.

I like your read-substring and write-substring.