Hardware compatibility within the XServe G5 range

The most obvious changes I can think of are CPU and memory.

The XServe G5 was produced with various speed CPUs over its lifetime, including 2.0 and 2.3GHz.

You will not be able to mix and match processors, so if your existing servers are 2.3GHz machines and the spare parts are 2.0 (or vice versa), you're out of luck.

The other change is that half-way through its lifecycle Apple added support for 2GB DIMMs. The early G5s would only accept 1GB DIMMs, so you might not be able to swap memory if there are 2GB DIMMs in the new machines and the older machines don't support them.
The only ways to tell if the machine supports 2GB DIMMs are to know the manufacturing date, or to look inside for '2GB DIMM' printed on the motherboard.
I'm sure there were other changes at that time, but probably not at the level that would affect spare parts (e.g. there may be other components on the motherboard that changed, but I doubt you're planning to desolder ICs to fix a problem, right? 🙂

In consequence, it would not be possible to replace a damaged system controller of our XServe with the one of such an "earlier" model ?

Well, yes, and no...

If you think about it, the 'system controller' is built into the motherboard. So if the system controller fails you're going to be replacing the entire motherboard, so it doesn't really matter whether the 'old' system controller is compatible with the 'new' motherboard since you're not mixing components at that level - you're going to replace the entire motherboard (that only supports 1GB DIMMs) with a different motherboard (that may support 2GB DIMMs).

Have you an idea whether or not Apple can tell me which internal revision the XServe we intend to buy is when getting the serial number of it ?

The serial number would definitely tell you if you know how to decode it.

IIRC the 2GB DIMM support was added in May 2005, so any machine manufactured after this date would support 2GB DIMMs - any before then would not. Bear in mind, though, that there may be some overlap, so if your machine was manufactured in exactly May 2005 it could go either way (likewise it's possible that machines manufactured in April also supported 2GB DIMMs as Apple started to ramp up production).

To find the manufacture date of any machine, look at the serial number. The first 2 characters are the factory ID (so ignore that), the third character is the year (so '5' = 2005, '6' = 2006, etc.) and the next two characters are the week number (so '18' = week 18 (the first week of May)).

So you should be looking for a machine with a serial number of xx518xxxxxx or higher if you want 2GB DIMM support).

I'd say both of these supported 2GB DIMMs.

The oldest machine was manufactured in week 26 in 2005 which was sometime in June, well past when 2GB DIMMs were standard

You can often find the spare parts kits on ebay. I saw several G5 kits there just yesterday. I think they were "buy it now" for $499. Not bad if it is the correct version for your HW.