There is an open bug w/ Esri for this issue...#BUG-000110249 The option to enable SOEs and SOIs on services published from ArcGIS Pro to ArcGIS Server does not exist in ArcGIS Server Manager or ArcGIS Pro. This applies to all SOEs/SOIs, not just Cityworks...any SOEs/SOIs constructed. The workaround they have is also not sufficient...which is to simply modify the resulting GIS Service via ArcCatalog. This has been shared w/ Esri...the workaround does not work if the GIS service was published as a web layer from Pro originally…at least, not in the current production version of 2.0.1...so basically if you want to be able to utilize any SOE, publish from ArcMap/ArcCatalog to begin w/…then you can enable the SOE capability in the dialogue while publishing from ArcMap or afterwards thru the Capabilities form for the service just published from ArcMap. This bug was discovered in both the current version of Pro, 2.0.1 (w/ ArcGIS Server Enterprise 10.5.1) & Pro 2.1 (w/ ArcGIS Server Enterprise 10.6 PreRelease).This appears to have to do w/ some config setting in a file read by ArcGIS server...something Pro just doesn't set, so ArcGIS Server can't do anything about it.
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