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Oops. I didn't read deeply enough.
Try adding these two format lines:
format1 %a: %W Trap (%q) Uptime: %#T%#v\n
format2 %B [%b]: Trap %#v\n
to your snmptrapd.conf. It turns out that these are the format strings defined for syslog, but the syslog handler is only used if you have no logging options; otherwise the "print to net-snmp log" is used, which uses the format that you see.