Traditionally, isos have always shown a gap between flanged connections, gasket or no... it's a schematic drawing, not a true-life detail. And ISOGEN (it's not CADWorx which is creating these) is all about traditional isometrics.

If you want "proper" spool isometrics you'll want to try some of the spool types (rather than "combined") which do a better job. Otherwise you should skip ISOGEN entirely, and export PCF to SPOOLGEN or other spooling isometric software.

If you're *not* making drawings for direct fabrication, step back a bit and don't worry about the small details. Let the guys in the fab shop do their job; when presented with overly detailed drawings will just ignore all that extra work you put in.