I know the R52 motherboard can be used in a 14.1" T43 but I was wondering if there are any advantages to using them? and are there any better ones to use, ie FRU number?

No real advantage...they are basically the same...but, some T43 boards have more powerful graphics.

+ optional FireWire port on some R52s. To use it in T43/p body you have to do a little chassis mod.

The firewire port from an R52 board will only fit in the 15" T43 chassis, between PCMCIA opening and fan exhaust.
The left side of the 14.1" T43 is too short to accommodate an extra port.
But you could do some really fancy DIY and put the firewire where the Infrared currently sits.
Or just rip out the firewire port altogether. It is only glued diagonally over the R52 PCMCIA cage.

Is the soldering the same? are they more or less prone to the Southbridge kind of failures?

burns

Same soldering...

I beg to differ.
R52 motherboards are a newer generation than the T43 motherboards.
When these came on the market, the lead-free soldering, as required by RoHS, was much better understood and applied.
It is very rare -to almost unheard of- that an R52 motherboard fails.