I was solely looking at performance, but you are correct in your post. Taking in other factors opens other avenues of decision making and a base GT cannot hold a candle to ST3's added amenities.

Pricing cheat sheet for a red Focus ST3 with moonroof and engine heater:

MSRP Invoice Dealer X-Plan(4)
Base: 23700 22100 20856 22100
Options: 5365 4788 4507 4788
ST3 net: 4435 3959 3726 3959
ST3 base: 4840 4320 4066 4320
ST3 discount: -405 -361 -340 -361
Moonroof: 895 799 752 799
Engine heater: 35 30 29 30
Vehicle total: 29065 26888 25363 26888
Destination fee: 795 795 795 795
Advertising fee: 436
Fuel fee: 42.72
X-Plan discount: -112.65(5)
Total: 29860 27683 26158 28049.07

Dealer Processing fee: 499(1) 499(1)
Plan Admin fee: 275(2)
Plan Document fee: 100(3)

Total: 30359 28182 26158 28424.07

Notes:
(1): Dealer#1 = 499, Dealer#2 = 489
(2): 275 is fixed for A-Plan and X-Plan pricing
(3): optional, 100 is maximum, unless state law mandates less
(4): using fordpartners.com calculator
(5): 0.004 * plan_invoice
plan_invoice = base + options + destination + advertising + fuel
= 22100 + 4788 + 795 + 436 + 42.72 = 28161.72

Ford holdback: 3% of configured MSRP = 0.03 * (23700 + 5365) = 871.95
A-Plan: plan_invoice - holdback - advertising + admin + document
28161.72 - 871.95 - 436 + 275 + 100 = 27228.77
X-Plan: (0.996 * plan_invoice) + admin + document
(0.996 * 28161.72) + 275 + 100 = 28424.07

Virginia taxes/title/tags:
State tax: 3.00%
Local tax: 0.17%
Title+Tags (Dealership): ~$85 (title and tags)
Title (DMV): $10.00
Registration (DMV): $40.75
Dealer markup: ~$35.00

Dealer price: 26158 OTD
A-Plan: 27228.72*1.0317+85 = 28176.87
Dealer#1 (X-Plan - 600): 27724.07*1.0317+85 = 28687.92
Invoice: 28182.00*1.0317+85 = 29160.37
Dealer#2 (X-Plan): 28424.07*1.0317+85 = 29410.11