Hi,

I think what we need to do is convert the local ENU baseline to a ECEF baseline.

Due to the original baseline is referred to ECEF, you should disable the ENU conversion.

I don't see how a topographer would be able to directly produce a ECEF baseline

Each GNSS receiver provides the position in WGS84. Here an example output of my u-blox sensor

The coordinates are given in Lat / Lon / ell. Height and can be simple converted to WGS84 X/Y/Z coordinates. If you observed two points, the baseline is derived by the coordinate differences.

unless they have some commercial software that has this feature

No, that's not right, see the screenshot above.

There seems to be a missing link between JAG3D and RTKLib

No, see e.g. page 14 in the manual: X/Y/Z components in ECEF frame. RTKlib supports ECEF. Just use it.

regards
Micha