MSI anticipated that RX 5600 XT would launch into a slot in the GPU market where there was no other competition, so it would be a good seller, especially at under the psychological $300 mark. Based on that they budgeted a certain amount of money to design a number of 5600 XT SKUs, covering the performance range from stock to just below 5700.
Then NVIDIA cut RTX 2060 prices by $30 and suddenly the 5600 XT was no longer competitive. AMD had two options, either cut RX 5600 XT prices in return, or increase the card's performance. Since 5600 margins are apparently quite slim as is, AMD chose to release a new higher-performance BIOS.
That means AMD and its AIBs aren't losing money on every RX 5600 XT sold, but it does mean that AIBs with more 5600 XT SKUs - e.g. MSI - are screwed. Because instead of being able to market cards at various points along the clockspeed (performance) range from 1375MHz/12Gbps to slightly over 1615MHz/14Gbps, they now have to start at the higher value. Which means their new "stock speed" card isn't 10%+ behind their fastest card, it's maybe 3%. Which suddenly means that half the 5600 XT SKUs designed by MSI have cannibalised the other half. Which means the design and testing and marketing time spent by MSI on those now-dead SKUs... is a loss for MSI.
There's no way MSI is going to sit back and just accept that. Over its lifetime, maybe the 5600 XT will sell well enough as a whole to recoup those costs. But... maybe it won't. And MSI is a business, it doesn't exist to break even, it exists to make a profit. So MSI is going to pad its 5600 XT prices to ensure it still makes a profit on these cards, which is probably going to make MSI 5600 XTs sell poorly, which is probably going to make MSI think twice about committing so heavily to buy so many AMD GPUs next time around.
On the flipside, you can bet that MSI and every other AIB is reaching out to NVIDIA in a frantic attempt to acquire defective TU104 chips so that they too can make an "RTX 2060 KO". That card is going to make EVGA filthy stinking rich.
(AIBs like Sapphire can afford to leave their 5600 XT cards at original pricing because they didn't design half-a-dozen SKUs, so they have fewer to write off.)
Honestly, the 2060 price drop was a masterpiece. It's an older card, so AIBs have long ago made back the money they spent to create their 2060 SKUs, so they won't mind too much that it's being price-dropped. It won't cannibalise existing SKUs because they're all old stock that's already been cannibalised by the 2060 SUPER. And of course, it gives NVIDIA-favouring AIBs a SKU that can compete with the RX 5600 XT, so they can make more sales.
Honestly it's a massive win-win for NVIDIA and its partners, and a lose-lose for AMD and its partners.
... another win for NVIDIA, and loss for AMD.
