[Bug] CLI Randomizer doesn't seem to verify whether alt formes can be used

[Fellshadow]

Describe the bug
The "Allow Alternate Formes" setting for e.g. Foe Pokemon gets applied when using the randomizer CLI to randomize a game that does not have the setting available in the GUI (such as Pearl).

To Reproduce
Steps to reproduce the behavior:

1. Prepare a settings file with "Allow Alternate Formes" enabled under the Foe Pokemon tab
   i. Load a rom such as Platinum into the randomizer GUI
   ii. Toggle settings, including "Allow Alternate Formes" in the Foe Pokemon tab
   iii. Save Settings
2. Open a command prompt
3. Use the randomizer CLI to randomize a game with the prepared settings file. Input ROM should be a game that does not support the alt form options, such as Pearl. Include the generate log file toggle
4. Open the log file and identify trainers with alternate formes of Deoxys randomized onto their teams (Deoxys-A, Deoxys-D, Deoxys-S). May need to repeat step 3 if there aren't any or to get a trainer that is easier / quicker to reach in-game
5. Open the randomized ROM in an emulator and battle the trainer(s) identified in step 4, verify the game freezes when it attempts to send out the alternate form of deoxys

Expected behavior
The "Allow Alternate Formes" setting is ignored/discarded, as the randomizer does when loading the settings file through the GUI

System (please complete the following information):

• Operating System: Windows 10 Pro 22H2
• Java Version: 1.8.0_431
• Randomizer Version: 4.6.0

Additional context
The issue was seen when someone in the ironmon discord attempted to play standard ironmon on Pearl, using the NDS tracker's new runs feature and this settings file which was made using the standard ironmon settings string and a Platinum ROM
Link to discussion in the ironmon discord

It only seems to be an issue when randomizing through the CLI and using a settings file that was made with a different game loaded into the randomizer GUI, so it's probably not a big issue since ideally you use a settings file made with the game you intend to play anyways. An easy fix user-end is to load the ROM you intend to randomize into the GUI, load the settings file, re-save the settings file, then use the result since the alt form settings get disabled when loading the settings file into the GUI