My personal opinion is that the flood stories not only of Gilgamesh, but those found in nearly every other civilization as well, are rooted in the same event, the flood of Noah. However, the various accounts were most likely developed independently. I believe the flood account of Genesis was written down by Moses many hundreds of years after the event. The account was probably communicated to him through a combination of divine illumination and tradition handed down from his forefathers. Abraham could have heard the account directly from Shem (or possibly Noah himself), and Moses was not too many generations removed from Abraham, so the purity of the account is guarded. This is my read on the question. You would be fascinated to spend some time reading the accounts of major floods in other cultures and to compare the features with the Gilgamesh epic, and the Bible account. For example, many tribes of American Indians have flood stories in their cultures.
The Gilgamesh epic itself was written after the Tower of Babel (out of which came the Babylonian civilization, of which Gilgamesh was a product). Although Moses wrote the events recorded in Genesis probably sometime in the 15th century B.C., the events he was recounting happened far before that, and far before Gilgamesh was written. The Gilgamesh epic is dated to about 1760 BCE. This would make the account within a three hundred years of the commonly accepted date for Moses. But even the most conservative reading of the geneaologies in Genesis would have Abraham 300 years before Gilgamesh, and the tower of Babel would have been during the lifetime of Noah, who died around the time of Abraham.
The Gilgamesh epic has all of the trappings of classical myth, with fanciful explanations given for events that were not explained within the science of the day. On the other hand, the story in Genesis is of a very different order. No fanciful explanations are given for incomprehensible events. We are simply informed that God did it, and there is a moral atmosphere to the accounts in Genesis that is missing from Gilgamesh and other mythological accounts I am familiar with. If the Scripture was in any way based upon the Gilgamesh account, it should be more fanciful, not more reserved, since derived stories tend to gain in folklore with the retelling. Reading the book of Genesis, I do not get the idea that it is derived from Gilgamesh, even though some of the events are superficially similar, and are doubtless tied to the same history. I think it is very clear, as you have surmised, that the accounts are related, but I encourage you to consider the possibility that they both had a common source in real events that were either witnessed (the flood, etc.) or were revealed (the creation).
A comparison of the two accounts used by Dr. Jensen can be seen here.
2010 Arthur V. Chadwick, Ph.D.