Next year we will overhaul the symbology system in GPlates to allow specifying a specific symbol/size/colour for each feature (point/line/polygon) using rules.
In the meantime you can use the GUI like you mentioned, or you can use the symbol file format currently in GPlates (but to be replaced by the above-mentioned symbology system next year). Have a look at the example symbol file in the GPlates sample data (in SymbolFiles sub-directory). It allows you to specify one of four symbols for point features based on feature type. Here’s the example symbol file (where it notes the restrictions):
# GPlates symbol definition file
#
# This file format will be short-lived.
#
# Each line of this file should be of the form:
#
# feature-type symbol-type symbol-size fill-state
#
# feature-type (text) should be the name of a gpml feature type, such as Volcano, HotSpot etc.
# (but do not prefix with gpml)
#
# Currently we only have support for features with point-like geometry,
# features with 'Position' in the Geometry Property panel of the Feature Creation Dialog
#
# symbol-type (text) must be one of:
# CIRCLE
# CROSS
# SQUARE
# TRIANGLE
#
# symbol-size should be a positive integer.
#
# fill-state is optional and should be one of:
# FILLED
# UNFILLED
#
# The default fill-state is FILLED.
# Not all symbol-types will respect the fill-state (e.g. CROSS)
#
# To use this file in GPlates, load it into GPlates through Features->Load Symbol file...
#
# Some restrictions on current symbol file usage:
# * Only one file at a time can be loaded
# * Symbol rules in the file will apply to all loaded collections.
# * Only point features will be drawn with symbols.
# * Symbol mapping is only by feature type.
#
MagneticAnomalyIdentification CROSS 2
Volcano TRIANGLE 4 FILLED
HotSpot SQUARE 3 FILLED
Seamount CIRCLE 2 UNFILLED