I hope the MSRP has not increased. I've been waiting for the 3900X to come back in stock and will not support scalpers. A higher MSRP makes upgrading less appealing.
I kind of doubt the MSRP has been raised. If that were the case, you would likely see more consistency in the pricing. The stores are probably just increasing prices to whatever they think people will be willing to pay. It's a lot like what we saw when there was a shortage of graphics cards last year due to crypto mining. The MSRPs didn't increase, but since the retailers were selling out of the cards as soon as they got more in stock, they raised prices to make the best of it. If no one else reliably has the product in stock at MSRP, and there are people willing to pay the higher prices, it kind of makes sense from a business perspective.
And paying a premium can still be considered worthwhile to many of the customers buying a processor like this. It may be on a "mainstream" platform, but the 3900X is clearly geared toward a more niche professional audience rather than mainstream users. For those whose profession can truly benefit from having a 12-core, 24-thread processor, paying a 15% premium on the chip can still be considered very reasonable when the closest competition from Intel costs twice as much. And if the higher price deters many of those who don't really have an actual "need" for such a processor, that could actually be considered a good thing for those that do, since it may be a bit easier for them to get hold of one. Someone buying a CPU for gaming, or general "enthusiast" PC use, might be better served by some other processor anyway, and if they really want one, they can probably wait until stock is more widely available some months down the line.
By the way, its worth pointing out that the 9900K was also unavailable at its MSRP for many months following its launch. Despite having a $488 MSRP, Newegg had it priced a very similar $580 for its first couple months on the market, and Best Buy only occasionally had it in stock for $530, based on PCPartPicker's price history graph. They don't list Amazon pricing, but I believe it was similar to Newegg's when in stock. Then, after a couple months, you started to see wider availability at more outlets, though it was still priced around $540-550, before settling around $530, where it stayed until about 6 months after launch, when it finally started dropping near its MSRP, under $500.
...the Ryzen 9 3900X has gone up in price in a little more than three month's time since the chip's release...
Shouldn't that be "less" than three months? Third-gen Ryzen only came out in July.