That's been my experience as well. At idle with no accessories running, it might break even, but most likely will not charge until you are 1/4 throttle or more.
Pulling the battery and charging it separately sounds like the way to go.
Starting with my KLR I've been installing volt meters on the bike. An led indicator that tells me if I'm undervolt, breaking even or over volt. When I tour I run a heated jacket, grips, gps and highbeams. It's peace of mind to know that I won't be bump starting it when I get there.
Check eBay, you can get them from $6 and up.
Older bikes and some not so old bikes, idle with barely 13V ... in that case yes you will have problem because the battery will be slowly getting depleted, but not until you start all kinds of things, like extra lights, heaters etc. and will keep idling without taking off. At some point, you will ride and the voltage will go up and your battery start charging, right? In that case your voltage should go over 14V and the battery will be getting re-charged. If you are not getting 14V min. you are having a problem in my opinion, unless it's by design, but that would be a bad design, no?