TG,
Sorry for the delay...
When we compared 5E3 x 5E9-A - same guitars, players, cabinets - the 5E9-A had more headroom indeed, however, I must point out that I built these amps, they are not dead stock layout - hey, diy'ers roll their own

- not clones from companies...
My personal 5E3 has around 285vdc @ 6V6 plates, while 5E9-A has ~360vdc. Of course this sets preamp voltages higher overall and could be a factor for it's "higher" headroom. Thus, 5E9-A has more dinamic range and sounded more controlled, however, less forgiving.
IMHO, 5E9-A is an outstading amp, as well as 5E3.
Regarding O.T.'s, I like to have 4-8-16 secondary outputs. Both amps were built as heads instead of combos and it offers more options to plug different speaker cabinets.
I did some mods to 5E9-A:
GZ34 tube recto;
Added choke to B+ G2 node;
22uF Solens on B+ rails;
Elevated heaters reference;
Metalfilm resistors;
Mallory 150 on preamp and OD 716 on P.I.
5E3 is all carbon comp, mallory 150 and F&T filter caps. Also heaters were elevated to ~100vdc reference.
Both amps had Tung Sol NOS 12AY7 (V1), Philips ECC83 (P.I.)
5E3 had G.E. 6V6GTA and Philips ECG 5Y3WGTA.
5E9-A had JJ 6V6 and Philips GZ34 metalbase - later changed to JJ GZ34, believe it or not it did sound better...
Best speaker for 5E9-A we have tried so far is WGS 15" Alnico...killer!!!
If I were to build another example of either amp, I would choose B+ ~ 340vdc and use new production tubes. G.E. did not like the higher voltages I had on my 5E9-A.
Hope this helps,
Best Regards,
R.