Apps built into custom ROM vs. installing cab's on clean install

[brockmo]

I am sorry if this has been asked before, and it probably has, but I cannot find it. I think I made the subject pretty explanatory though as far as what I'll be asking.

What are the benefits, if any, to install a custom ROM like Colonel's for example with a boat load of apps BUILTIN to the rom as opposed to just installing the cab's I would want on a very clean ROM of my choosing? Can anyone help me out here and briefly explain? Are there performance benefits... anything? What I've noticed is if you have a custom ROM with an app built in that is frequently updated (S2U2) then you are kind of gambling as to how the app will work if you install the new version right over top of it... can anyone provide some insight on this? What are the pros/cons of having apps built into a ROM vs installing the cab yourself. Thanks in advance...