William Marvel's "Lee's Last Retreat" (2002) indicates that the march order started with the CS Independent Signal Corps remnant (1 man from the 1st Co. and 44 from the 2nd) trailing along after the Provost Guard, whereas the Naval Battalion[sic - per Marvel] of 124 officers and men, plus one from the Reserve Naval Bn and 28 CSMC [I'm using numbers from Nine and Wilson's "The Appomattox Paroles," Va Regt'l Series, 3rd edition] marched separately as part of Custis Lee's division, as you state. (Have you noted any case of CSMC or CSN using an ANV-pattern flag?)
The ISC men represented Major Milligan's two-company (plus tiny HQ) unit from Petersburg that had manned commo and observation sites along the James and Appomattox from the Drewry's Bluff-Chaffin's areas down. (I'm still curious whether they would have merited an ANV infantry-size battleflag, whether as an independent demi-battalion commanded by a major, or virtually integrated into the ANV as it closed on the Petersburg area in the last months of the war. Is there a precedent?) Although an army unit, they also had army signalmen on ships of the James River squadron to facilitate ship-to-shore comms. Milligan, their C.O., was ex USN and US Revenue Service lieutenant who had initially been in the Virginia Navy and set up a signal system for local defenses in Portsmouth-Norfolk area, then switching to army and changing base to Petersburg. (If you can justify it, his unit might be best suspect for a battleflag -- unlike the "regular" Signal Corps, they were armed and fought, occasionally as infantry.)
Marvel (p. 35) gives the impression that the bulk of Tucker's naval unit -- and the Marines -- came from Drewry's Bluff, rather than ship's crews from Richmond station. I haven't sorted them out.
I do not readily find a Private (or other rank, army, navy, or Marine) B.C. Casey in anything readily available to me.
The Lane claim, for which he eventually (1866) received the Medal of Honor, identifies the flag he took as being that of the Nansemond, which would seem to have been the ensign you note.
We seem to have a confused situation here, during the worst possible time to expect order and complete accuracy. Better flag Howie's notes for special attention when you return to them.