Others can explain much better than me, however this is due to the chip capacity being 8MB.
You have 3MB of the actual firmware, plus another 5MB of nothing, which is simply there to fill the rest of the chip.

On November 11, 2019 9:58:44 PM GMT+02:00, Jochen van Waasen <jochen@vanwaasen.ch> wrote:
Hi

I would like to use your tool to mod my bios.

First step would be to create a backup of my BIOS:
# dmidecode 2.12
SMBIOS 2.7 present.
66 structures occupying 2563 bytes.
Table at 0x000EB4C0.

Handle 0x0000, DMI type 0, 24 bytes
BIOS Information
Vendor: American Megatrends Inc.
Version: 4.6.5
Release Date: 10/11/2013
Address: 0xF0000
Runtime Size: 64 kB
ROM Size: 3072 kB

When I read that correctly the ROM Size is 3072 kB

# flashrom -r RDD516-NT.rom --programmer internal
flashrom v0.9.7-r1782 on Linux 4.4.184.x86_64.1 (x86_64)
flashrom is free software, get the source code at http://www.flashrom.org

Calibrating delay loop... OK.
Found chipset "Intel C206". 
This chipset is marked as untested. If you are using an up-to-date version
of flashrom *and* were (not) able to successfully update your firmware with it,
then please email a report to flashrom@flashrom.org including a verbose (-V) log.
Thank you!
Enabling flash write... Warning: SPI Configuration Lockdown activated.
OK.
Found Macronix flash chip "MX25L6405(D)" (8192 kB, SPI) at physical address 0xff800000.
Found Macronix flash chip "MX25L6406E/MX25L6436E" (8192 kB, SPI) at physical address 0xff800000.
Found Macronix flash chip "MX25L6445E" (8192 kB, SPI) at physical address 0xff800000.
Multiple flash chip definitions match the detected chip(s): "MX25L6405(D)", "MX25L6406E/MX25L6436E", "MX25L6445E"
Please specify which chip definition to use with the -c <chipname> option.

Which chip should I select?
When I select one chipset a 8MB file is created. Shouldn’t a ROM back be only 3072 kB?

Any help is appreciated.

Best Regards
Jochen