I seem to have stumbled on an issue with the ipsec implementation on OpenBSD. While trying to configure manually-keyed transport SAs between hosts on the same subnet, I discovered that NDP appears to fail. Specifically, it appears that one endpoint will briefly learn the L2 address of the other endpoint, while the other host ndp cache never learns the address. This results in behavior where icmp6 traffic is encrypted in one direction (ironically, it is the traffic transmitted by the host that never appears to learn the address of the other), and not in the other. A tcpdump shows the following pattern:

20:48:22.518275 08:00:27:42:35:6a 33:33:ff:00:00:02 ip6 86: fc0a:4600::3 > ff02::1:ff00:2: icmp6: neighbor sol: who has fc0a:4600::2(src lladdr: 08:00:27:42:35:6a) [icmp6 cksum ok] (len 32, hlim 255)
20:48:22.519842 08:00:27:31:0f:52 08:00:27:42:35:6a ip6 142: esp spi 0xa753d86c seq 801 len 88 (len 88, hlim 255)
20:48:22.521577 08:00:27:31:0f:52 08:00:27:42:35:6a ip6 142: esp spi 0xa753d86c seq 802 len 88 (len 88, hlim 255)
20:48:23.521836 08:00:27:31:0f:52 08:00:27:42:35:6a ip6 142: esp spi 0xa753d86c seq 803 len 88 (len 88, hlim 255)

Some searching turns up a conversation on the OpenBSD mailing lists that appears to describe the same behavior. However, it appears that there was never a consensus on the solution, and thus one was never implemented. I did find a hacky workaround that gets IPSec working between the two hosts. By setting static ndp entries for the remote host, there is no need for neighbor discovery to run, and the transport works.

root@net70-3[][20:51:37]:/etc ndp -s fc0a:4600::2  08:00:27:31:0f:52
root@net70-3[][20:51:58]:/etc ndp -an                                
Neighbor                             Linklayer Address   Netif Expire    S Flags
fc0a:4600::2                         08:00:27:31:0f:52    vio1 permanent R 

For reference, the following is my SA configuration. The spi and key values are the same in both directions, as I was working towards trying to make OpenBSD protect OSPFv3 traffic (I am still unsuccessful).

flow esp from fc0a:4600::3 to fc0a:4600::2 
esp transport from fc0a:4600::3 to fc0a:4600::2 spi 0xa753d86c:0xa753d86c \
 authkey $akey1:$akey1 \
 enckey  $ekey1:$ekey1