I think the problem is with the COA, not the fact that it is a pen made from a JD barrel. I had a look at the COAs of JD blanks supplied by other vendors and they are nothing like the one you have. Their COAs are plain and just state that the wood used is from a JD barrel.
The COA you seem to have has a couple of lines that might imply that JD had some direct involvment with the making of the pen. Plus the blatant use of their logo and font. They are protecting their trademarks and reputation.
I had a similar situation many years ago when I had an internet provider business. I had a customer with a permanent dial-up connection, who asked to have the connection named "I-like-
popular cola". A few months later I got a fax from
popular cola's lawyers. When I rang them, I was told that it was possible that anything that customer said or did using that connection name could be misconstrued as comming from
popular cola and so damage their brand or reputation. Seems these companies employ people specifically looking for breaches of trademark or anything that might affect their brands reputations.
As a side note, none of these COAs (JD, JB, BOW, etc) can actually prove the providence of the blanks. Anyone could get this type of COA printed up. You really need tracable signatures or official stamps.