Webmaster, the Gap theory is based on two things:
1. The 'need' for evolution and radiometric dating to show vast billions of years, and
2. The obvious difficulties geologically in trying to fit all of the strata and fossils into the "one flood did everything" model which is current among many YEC's -- which means our geologic record had to build up in one year.
However, the language of Genesis does not support a Gap theory, and neither does theology or geology. Contrary to your link, there is no vast mystery in the geologic record -- there are simply different explanations for what we are seeing. There's quite a difference there.
Genesis 1:1 states the fact of creation. The next verse narrows the focus to the earth, which at the point of initial creation did not have concrete shape or intrinsic organization. The rest of Genesis 1 tells how God progressed in creation from that condition.
The Gap theory indicates the earth was first created, populated, and then suffered rebellion, sin, and destruction due to Satan and his followers. This then resulted in a destroyed earth which was then 're-created' by God in the Genesis 1 account.
This places Satan as a fallen being before Eden. Yet the Bible contradicts this. Read Ezekiel 28, where God is speaking through Ezekiel to Satan, through the King of Tyre:
You were the model of perfection,
full of wisdom and perfect in beauty.
You were in Eden, the garden of God;
every precious stone adorned you:
ruby, topaz, and emerald, chrysolite, onyx, and jaspere,
sapphire, turquoise, and beryl.
Your settings and mountings were made of gold;
on the day you were created they were prepared.
You were anointed as a guardian cherub,
for so I ordained you.
You were on the holy mount of God;
you walked among the fiery stones.
You were blameless in your ways
from the day you were created
till wickedness was found in you."
vv12b-15
The standard Gap theory also says the majority of the fossil record is the result of the destruction at the end of the Gap. Geology absolutely refutes this in terms of the time element, no matter how you cut it. There is no biblical mystery about the Pleistocene - Holocene boundary. This is the time of the Ice Age of Job and is clearly chronicled in the Bible.
The Gap theory is an invention of man and depends on trying to criticize other ideas as well as a rather extensive 'reinterpretation' of the Bible.