I have sat on the side of this because opinions are so strong on this issue. But sometimes facts get skewed as opinions form. Frankly I think much of this is border line insanity on the issue.
First I can say I see an awful lot of MTH trains for repairs. I dive into them pretty deep when I started, and I have a pretty good memory and such, and keep good notes from when I started. I dissected and reverse engineered the boards well before even MTH was providing details on how to fix things beyond what the ASC Service manual said, and in fact I provided feed back on the book to correct many errors in diagnosing 3V faults. Especially the Power Supply board.
First, I have seen PS-1 and PS-2 5V come in with original MTH White Batteries that still hold sufficient enough charge to operate the engines in conventional. I have also seen them dead as a door nail and not hurt the boards.
So lets add some facts as I see them, and folks with deeper Electronic backgrounds can fact check me if I have misstated something.
Boards up until PS-3 designed to work with Battery not BCR.
MTH 9V batteries are 180 mahr batteries. But this is just the charge they can provide. Has nothing to do with how fast or slow they charge.
The PS-1 and PS-2 5V boards are operated on 5VDC. So a 9V battery is stepped down to provide backup power. It is also isolated in how it does it with current limiting resistors and transistors for turning on an off. So how is a bad battery killing a board other than some how maybe damaging the charging circuit.
All these microprocessor have protection circuitry, even PS-1 to prevent damage to the chips in the event battery backup or even power supply power is not sufficient, or too much. For PS-1 issues it typically is that the voltage is just low enough to still operate the chip, but not high enough that data can be stored correctly to memory when shutting down. This typically leads to a software conflict/ID conflict especially on earlier boards. Later boards had different software and far less subject to software issues that would not resolve from shutting down and waiting a few minutes before restarting.
PS-2 5V have there own set of problems and many of the circuits that are made up to make a complete board run very close to design limits. It was the first of its kind and build from 90's tech, but pretty state of the art for toy market. So you see all kinds of failures and frankly not necessarily related to the capacitor issue we like to debate also, but in my opinion not the battery either. Some models really had a higher failure rate then others and it did not necessarily carry over to every train made that model year. No one has really done a compete failure analysis. So what are we doing? We buy insurance.
PS-2 3V is a far more robust design with much improved component and design work. It operates a processor on 3.3V, so that 2.4V battery has to step up voltage to make things work. The source of the 3.3VDC gets power from a 5VDC PS that I have seen smoke with a short. Fix the short and that PS still works fine. The battery sources that 5V PS when track power is off. Both have specific protection built in to protect the chip. In the thousands of boards I have repaired I think I have replaced 1, yes 1 5V power Supply and just 2 3.3VDC PS. The only way you kill the board is putting AC on the DC Circuit of the board. But that only kills the DC Components and processor chips that run the logic. AC on the DC circuit and those power supplies still put out correct voltage. It is the audio amp, speed control, logic chips, processors that get damaged beyond repair.
So lets get to the BCR. Charging circuit is basically 2 functions. One is charge the battery or in this case BCR. Other is cut backup power in and out when Track power goes away. Independent circuits with some co-dependency. You can get one or the other failure, or both. For PS-2 3V, there is one other circuit. The boost. Control of the inductor charging that adds the extra 2.5VDC to the battery 2.5VDC to make 5VDC for the Power Supply. If that fails, a battery won't work because the voltage is insufficient, but a BCR will work, because the BCR Charges to a 5VDC level. So the boost is not necessary. So that is why some of you have seen engines not work with Battery but does work with BCR. If the charging element is bad, the BCR won't work because it can't charge, but a battery does because it has a charge. Works until battery charge is gone. Then you need to externally recharge battery. If neither work, most likely the circuit that cuts in and out the backup power has failed.
Again, I see far less 5V charging failure in all these years. Whether BCR or battery. Was it designed for bcr? No. Do they work? Yes. Same with PS-1.
PS-2 3V has a very robust Power FET used to control battery. Can it fail. YEP. How? Normally crushing the battery leads to the chassis. Or some other AC on the DC circuit I talk about that kills the logic chip that runs the charging and cutting in and out FETs. All repairable because of the board design, unless traces have burned up. Why I see more damaged charging circuit failures in 3V then 5V is how the system works and that FETs are used to limit current charge and charging of the inductor boost. When the logic chip is damaged it can tell the fet to conduct fully and when that happens you start drawing higher amps at startup that starts to smoke that 5VDC power supply until the fet burns up and opens.
There are far too many engines out there (PS-1 through PS-2 3V) running on BCR and Batteries of all sorts to think your engine failure was because of them.
Defective BCR that is shorted will be a problem. That rare battery that some how fails and acts like a direct short, same thing.
But you will damage your engine far more via derailments, maintenance the crushes wires on reassembly then from installing a battery or BCR.
Hey I even saw a PS-2 3V upgrade that the person used the a 9V battery on and the board and charging circuit was not damaged.
So stop worrying about this and just do what you want. Lets debate the best grease and oil for lubrication. 
G
