I agree. Also, as far as the CNS not being awake until later in the day, this does have some truth to it. However, the CNS can be awakened through a proper warm up.
So, basically you're going to need a more intensive and complete warm up earlier in the day than you would later in the day (when your body/CNS is already awake from performing your daily routine). But, that's really the extent of it.
Right, most people train at the same time week in and week out because that's what their schedule allows. If you've got all the time in the world, then just try training at different times during the day and see which you like best.
But, once you find a time that works, try to keep that general time consistently. It really doesn't matter if on Monday you prefer training chest at 6AM, and on Tuesday you like training legs at 4PM, and on Wednesday you like training back at noon. Just so long as you keep those times relatively consistent.
Personally I've tried just about everything out there; high volume/high intensity/low frequency, high volume/low intensity/low frequency, low volume/high intensity/low frequency, low volume/high intensity/higher frequency, etc...etc...etc...
Really there are so many options out there and everybody responds differently to different programs. One other thing to consider is that some programs are directed towards advanced trainees (those who have been doing this for a while and have built a decent strength base), while others are designed with beginners in mind.
If you're a beginner, you should stick to beginner programs. Even though the advanced programs would still work (in theory), you probably don't have the experience, work capacity, and/or strength to make them really worthwhile.
Right now I'm doing low volume/high intensity/higher frequency and am enjoying it a lot. But, once again that's just me and where I am in my development right now.
Hope this helps.