The Weatherby vanguard is no less safe to handload for than any other modern bolt action.
The warning about Weatherby chamberings has to be put in the proper context. "Back in the day", Weatherby chamberings were popular among gunsmiths both professional and garage types (one of the early "magnum" line of chamberings through the 40's and 50's), for rechambering from "standard" calibers. One of the more common found was 30-06 rifles rechambered to 300 Wby mag. It would dramatically depend on where that reamer came from and who did the chamber reaming as to how much "free bore" the rifle had. Some of these rechambered rifles were down right scary. I recall seeing a blown up Springfield 03 in an article some 20 odd years ago.
The vanguard is made to Weatherby's chambering specs, and Weatherby stands behind the rifle to be safe to shoot with the corresponding factory Weatherby ammo. So what I'm trying to say is, the vanguard is just as "safe" to shoot with handloads as a mark V rifle is. The biggest issue is MAKING safe handloads...
You still have to take all the same care with either rifle (mark V or vanguard) when you develop your handloads. I have a vanguard in 257 Wby mag myself. I've never fired a factory round down the barrel. My handloads are loaded to SAAMI spec max over all length, and they chamber perfectly in my rifle. My powder charge is slightly below the "max" listed in my reference reloading book, as are most of my own handloads. The last thing you want to do is start off your load development by just cramming the case full of a "max" load and seeing what happens when you pull the trigger...
That could be a bad day no matter what rifle or caliber you're working with.
Each and every rifle that comes down an assembly line is it's own unique individual rifle and should be treated that way. You should always start your load development well below the "max", and work your way upwards in slow increments until "your" rifle tells you when to stop. Either by too much pressure, or too poor of accuracy, or you hit the "just right" recipe that makes your rifle print the accuracy you're looking for. Very often what happens is that a particular recipe of bullet, primer, powder, that works great in "rifle A", will not shoot worth diddly crap in "rifle B" (even in the same brand and model rifle). That's just part of handloading.