I would say it’s just an archaism, and not so very old. Check out the AHD etymology I link to above, which derives (with the qualifier “possibly") the fecal sense of “poop” from an earlier usage meaning “to break wind”.
The OED simply considers these meanings two senses of the same word, and doesn’t even give them separate subheadings:
3. slang (orig. nursery). An act of breaking wind or of defecation; (concr.) faeces; (fig.) nonsense.
1888 Stag Party 193 When Alcy pooped, the poop was mostly tallow. 1937 E. PARTRIDGE Dict. Slang 648/2 Poop,..a breaking of wind. ...
That, BTW, is from the 2007 draft revision, so it presumably reflects up-to-date research.