Questa Simulation Not Showing All Needed Variables

It's probably a good thing to read msim_setup.tcl and create your own startup call into that, using ld_debug and enum_debug as shown in the verbose output from the setup tcl. But I wouldn't go so far as to modify them directly as they can get recreated by Quartus.

Here's my normal startup:

do ../mentor/msim_setup.tcl
set TOP_LEVEL_NAME testbench_test
set FORCE_MODELSIM_AE_SELECTION true
set SILENCE true
elab_debug -suppress 3016 -t 1ps
do wave.do

and my rebuild when I create a new IP module in quartus and generate a new script for msim.

do ../mentor/msim_setup.tcl
set TOP_LEVEL_NAME testbench_test
set FORCE_MODELSIM_AE_SELECTION true
set SILENCE true
ld_debug -suppress 3016 -t 1ps