Does anyone know why the RT3 has two holes drilled in the headlight bucket? The first one is for the High Beam but not sure what the second one is for.
I expect Yamaha used the same bucket for many models.

My guess is the speed warning lamp that became mandated in Japan about that time.  I don't know if any other countries got it?  

"My guess is the speed warning lamp that became mandated in Japan about that time."

Yes, I agree with Mark.

A handful of Japanese Domestic Market (JDM) bikes were brought back to the US by returning servicemen and, as they got sold on to new owners, that red light caused lots of confusion!

Just out of interest, I bought a set of JDM TX500 clocks which have that red light in the centre of the bracket and, when I get the time, I want to sort the wiring out then spin the speedo up with a drill, to see if the light still works. As well as the red light, there is also a red line on the speedo at 80kph.

It's not just the RT3. Many Yamaha enduro's have 2 holes with a rubber plug in the lower one. Including my 68 DT1 250, 69 CT175 and 70 RT1 360 and many more bikes that i have owned like the 69,70 and 71 DT250's. Odd enough my 69 AT1 doesn't have 2 holes. Only one for the high beam indicator. Go figure!  

I wonder if the AT1 was considered not capable of exceeding 80kph, and so no need for the warning light?

Skydancer makes a good point.  

It's really hard to find information on the speed warning light they used in Japan.  As far as I can tell, it wasn't mandated by law until 1974 or 1975 though some bikes had them before that.  I can't remember ever seen a Yamaha Enduro Japanese model parts manual or wiring diagram that showed a speed warning light earlier than 1974.

Similar to how turn signals generally weren't required in the USA on motorcycles until 1973 but Yamaha included them in 1971.  (Note that turn signals were mandated in Japan several years earlier, but not included on most "export" models)

I'm going to change my guess and say there may have been some archaic law that required certain warning lights MUST be located on the headlight bucket.  (Note that early Japanese models (1960's) pretty much had the gauges and warning lights all integrated into the headlight bucket.)

Eventually, the gauges were separated from the headlight bucket and a few years later, the high beam warning lamp was moved into the gauges.

So my first guess is the extra hole was for a warning lamp (turn signal? battery charge? neutral?) that was required to be located on the headlight bucket in some countries/areas? 

But then there is another anomaly.  The 7" buckets (street models) and 5" buckets (AT1 and other smaller bikes) from that era do not seem to have the extra hole.  Maybe the 5 3/4" bucket was used on a model that needed the extra hole for something?