Traditionally alternators haven't been used to drive rectifier loads into capacitors. The traditional rectifier load has been resistive or inductive ( machine fields).
Once you go to capacitive loads the machine is expected to deliver its power in short rectangular pulses during the time when the relevant phase voltage is above the mean dc. The peak phase currents are high for a given rms value. This impacts badly on efficiency and stator stress ( including noise).
I can't see any difference between battery charging and grid tie except for the grid tie being much higher voltage and hence the line resistance will have negligible effect.
By using some form of power factor rectifier you can maintain a reasonably sinusoidal ac current into the rectifier. I really can't believe that changing one conventional rectifier for a bigger one will make any difference but if the commercial rectifiers are something like the Vienna rectifier that incorporates power factor correction then of course it will have a very marked effect.
Another factor may be the way the protection box works. If it limits volts by clipping on the ac side of the rectifier then it may be partially clipping even in normal operation. Short of looking with a scope at the machine 3 phase input I don't know how you can prove this but if it is clipping peaks then noise will be very likely.
Adding some inductance between the rectifier output and the inverter input capacitors will increase the conduction angle of the rectifier and improve the mean to rms current ratio and may dramatically reduce the noise but this may not be effective if the protection box is clipping peaks in normal operation. You may have to prove this on a day when you could safely run without the protection box if the choke gives no improvement.
The case is worse for an air gap alternator, all iron cored machines have significant leakage reactance and this causes overlap on the rectifier with a lengthening of the conduction period.
you could possibly try adding small ac reactors in the ac lines to simulate leakage reactance and force the rectifier to overlap but the inductance values will have to be small or you will get the undesirable reactance limiting characteristic of the iron cored machines.
If you go to a power factor rectifier such as the vienna or other forced commutated versions you can overcome some of this reactance limiting effect but the rectifier should then cure the noise anyway so ac reactors would be pointless.
These elaborate rectifiers are very lossy with too many diode drops at low voltage but should be excellent for the higher voltage grid tie, but they have fairly elaborate control circuits and you may need to involve SMA or someone who really understands these things unless you are a bit of an electronic wizzard ( it's basically inverter technology and ought to be part of the inverter but is probably too costly for small set ups).
Flux