I noticed the same thing a long time ago on my v9.x.x LTM's, but haven't actually migrated enough to my v10 to know if they are different.
Unless you have implemented Administrative Domains and Partitions on your LTM, then it won't make a difference if the node does not appear in the bigip.conf's node list.
The node(s) list created in the Configuration Utility is a list of specifically entered nodes (that appear in the bigip.conf) and the members of all of the pools listed in the bigip.conf.
It becomes important in Administrative Domains and Partitions because nodes not specifically placed in a partition will be "put there" during the configuation load of the F5. This becomes a problem if Pools in different partitions attempt to use the same servers (which violates the boundary limits of ADP (Partitions can only share resources within the same Partition or the Common Partition)).
In these cases you must specifically create the "shared servers" in the Common Partition for use by all Partitions. Doing this specifically causes an entry into the bigip.conf.
Naming a server in the Nodes area so that its name appears next tothe IP Address in the Pool Members view, also creates and entry into the bigip.conf.