"The process of transformation" could refer to either the re-tooling of America's military, as suggested by "911myths".
It could also refer to a "military takeover of the Middle East".
It could also refer to "both".
In strictly logical terms It could refer to "neither", although that appears to be an unlikely option.
If, as suggested by "911myths", the "Rebuilding America's Defenses" essay referred to "retooling America's military", then why would these ongoing efforts be such a controversial issue? Common sense tell us that the adoption of new technologies, (ie the said "transformation") in military organizations happens by default, and as such does not warrant a "catalyzing catastrophic" incident as suggested.
The Pentagon/DoD has always enjoyed a virtually limitless budget to keep ahead of the rest of the world: US military spending, has for a long time has rivaled the combined military expenditure of the rest of the world (including Russia and China), and now stands at around 42% of global military spending (!). Politicians from both sides regard cuts in military spending as a "no no", especially if it threatens jobs in their state, district or city.
Prior to 9/11, some of the first items on the Bush Jr. agenda (January 2001) was preemptive war against Iraq and Afghanistan. The 2001 Bush cabinet was loaded with the same people who authored that same R.A.D. document. They are all heavily invested in the US military-industrial complex. They are all hardline pro-Israel activists, many being dual US-Israeli citizens. They openly promote the "Zionist" political ambition ie the establishment, by force if necessary, of a "Greater Israel" within the MidEast. They also happen to be universally Islamophobic.
The explanation fe "transformation" put forward by alternative "911 groups" has far more traction that the "911myths" baby formula/ conspiracy yarn/pabulum. The key to 9/11 is all about motive. It's hardly surprising that the all important parameter of "motive" has been systematically excised from discussion of the 9/11 attacks and subsequent actions/effects.
The "they hate our freedoms" motive, put forward by President Bush just after 9/11, sounds like guilt transference, aimed at the demographic group/faith (Arabs/Muslims) towards which the US establishment has, for decades, demonized.