First off, yes, you need to check the open voltage of any new lithium coin battery after you first break it out of the package, and before you install into the meter. Some batts might have sat on shelf for a long time and no longer have full capacity.
Replacing the stock meter with a Voyager GPS unit was one of the first things I did after I got my 300RR. Trail Tech had them on sale over Xmas - $200 shipped for the full kit - so it was a no brainer. Stock meter doesn't even have tach. Anyhow, I ran the 12V+ power lead directly to the starter battery, so the meter is always kept fully charged and never draws from the "back up" 3V lithium. I also installed Battery Tender charge lead on every bike, so I keep the starter batt topped off also.
If you prefer to keep the OEM meter, consider getting a Molex 4-pin connector (.062") and reroute your power to the starter battery.