The phase noise of the E4406A is quite good but there's a lot of high performance options for measuring phase noise these days...? it's hard to keep up with it all. For many years I've wanted an Agilent E5052A SSA as used at my place of work. However, I may end up buying one of the modern alternatives for a fraction of the price!?
If you watch an E4406A or a PSA when they are booting, you can see it testing the IF preselector filters. It will say something like aligning LC Prefilter Wide, LC Prefilter Narrow, XTAL Prefilter Wide, XTAL Prefilter Narrow. I've not used a 12 bit E4406A but I assume it will still have these preselector filters.
The MXA will have them as well and it will probably flash up on screen messages when aligning or testing them.?