That's one option. Another option is organising plug-ins by which family they apply to.
For example, if 5 of them apply to
myFamily, then if this instance is collected via the command-line, then only those plug-ins would run.
You could, for example, have one directory with only plug-ins related to collecting from the command-line, such as image sequences or
.obj files, and append this to your normal
PYBLISHPLUGINPATH when running from the command-line. This collector could be responsible for assigning an appropriate family to the collected instance, such that the plug-ins you want to have run on it are discovered and run.
Also don't forget you can explicitly create/call plug-ins with a minor Python script.
from pyblish import util
from pyblish import api, util
all_plugins = api.discover()
relevant_plugins = list(plugin for plugin in all_plugins if "thisFamily" in plugin.families)
Hope it helps!