Hi,
I chose an epub I had and loaded it into calibre and converted it to .mobi, and then used mobiunpack.py to simply look at the structure of the resulting .mobi.
I took the same .epub and converted it using kindlegen (for Mac) to a .mobi and then used mobiunpack.py to examine the structure of the resulting mobi.
Here is what I found (any unknown metadata keys are shown as numbers and their associated values as hex strings)
Kindlegen Generated .mobi
Unpacking Book ...
number of sections 467
0 3816
1 12484
2 13577
...
length of this header 232
book title offset 456
offset to start of extended header 248
extended header length 208
extended header num_items 9
MetaData
ISBN -> 978-0-385-53313-3
Creator -> Dan Brown
Publisher -> Doubleday
Rights -> Copyright 2009
300 -> 03000000000000000000000000000080002000000000000000 00000000000000ecbef4ed01e001fc01a901b5409440934099 4098409c409d
204 -> 000000ca
205 -> 00000001
206 -> 00000002
207 -> 0000821b
Here is the same information for the Calibre generated .mobi
Unpacking Book ...
number of sections 354
0 2912
1 3472
2 4656
...
length of this header 232
book title offset 544
offset to start of extended header 248
extended header length 292
extended header num_items 12
MetaData
Creator -> Dan Brown
Publisher -> Doubleday
ISBN -> 978-0-385-53313-3
Published -> 2011-04-15 15:25:24+00:00
Contributor -> calibre (0.7.54) [
http://calibre-ebook.com]
Rights -> Copyright 2009
ASIN -> 0f7dd9a0-003a-45d8-9c87-c2adcef46ca1
CoverOffset -> 11
202 -> 0000001d
203 -> 00000000
501 -> 45424f4b
Updated Title -> The Lost Symbol
So it appears that the used up space of the extended headers are similar, although KindleGen seems to create some unknown MetaData keys/values: 204, 205, 206, 207, and 300. I will look online to see what these keys are actually for.
The biggest difference seems to be the size of section 0. For the Kindlegen generated mobi, section 0 is 12484 - 3816 = 8668 bytes long, whereas for the Calibre generated mobi, section 0 is 3472 - 2912 = 560 bytes long.
I am not sure what else is found in section 0 besides the extended header but the size difference is quite large.
So perhaps, what Amazon is referring to is the size of section 0 or the fact that certain metadata key/values are missing?
Hard to say without more information.