If you want to edit the config.txt file, you can edit it after the image build. Insert the SD card that has the image flashed. You will find the config.txt file in EFIESP drive like this:

Reference: "R-Pi configuration file" and "CONFIG.TXT"
Update: Building IoT Core image with the modified config.txt file.
The config.txt is provided in a package (RASPBERRYPI.RPi2.BootFirmware.cab). So we need to regenerate the RASPBERRYPI.RPi2.BootFirmware.cab with the modified config.txt file. You can follow these steps:
- Get all files needed to build the RASPBERRYPI.RPi2.BootFirmware.cab and copy them to a folder, for example,
D:\NewCab
. You can find them in EFIESP drive(You can find EFIESP drive in the flashed SD card):

- Edit the config.txt.
- Generate the new CAB file using this
RPi_UEFI.pkg.xml
file:
<?xml version="1.0" encoding="utf-8"?>
<!--
Copyright (c) Microsoft Corporation. All rights reserved.
-->
<Package xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema"
Owner="RASPBERRYPI"
Component="RPi2"
SubComponent="BootFirmware"
OwnerType="OEM"
ReleaseType="Production"
Platform="RPi2"
Partition="EFIESP"
BinaryPartition="false"
xmlns="urn:Microsoft.WindowsPhone/PackageSchema.v8.00">
<Components>
<OSComponent>
<Files>
<File
Source="bootcode.bin"
Name="bootcode.bin"
DestinationDir="$(runtime.root)"/>
<File
Source="config.txt"
Name="config.txt"
DestinationDir="$(runtime.root)"/>
<File
Source="fixup.dat"
Name="fixup.dat"
DestinationDir="$(runtime.root)"/>
<File
Source="fixup_cd.dat"
Name="fixup_cd.dat"
DestinationDir="$(runtime.root)"/>
<File
Source="fixup_x.dat"
Name="fixup_x.dat"
DestinationDir="$(runtime.root)"/>
<File
Source="kernel.img"
Name="kernel.img"
DestinationDir="$(runtime.root)"/>
<File
Source="LICENCE.broadcom"
Name="LICENCE.broadcom"
DestinationDir="$(runtime.root)"/>
<File
Source="start.elf"
Name="start.elf"
DestinationDir="$(runtime.root)"/>
<File
Source="start_cd.elf"
Name="start_cd.elf"
DestinationDir="$(runtime.root)"/>
<File
Source="start_x.elf"
Name="start_x.elf"
DestinationDir="$(runtime.root)"/>
</Files>
</OSComponent>
</Components>
</Package>
Start IoTCoreShell-arm.cmd
in the iot-adk-addonkit and navigate to the path D:\NewCab
and run the following command:
pkggen RPi_UEFI.pkg.xml
You will get a RASPBERRYPI.RPi2.BootFirmware.cab
in the working folder.
Use the new generate RASPBERRYPI.RPi2.BootFirmware.cab
replace the default one in this path C:\Program Files (x86)\Windows Kits\10\MSPackages\retail\arm\fre
After that when you build image the edited config.txt will be added in.