I believe the purpose is to reduce or punish dry passing so that each round actually counts, which is a common complaint. I certainly see your point and concern, however, it could add a new layer of complexity. I don't think it will kill engine decks, after all they like a long round and that will still be possible.
Dry passing R1 is a symptom of the coin flip issue. No one would intentionally cede control over their fate unless forced to by the imminent threat of losing CA. Furthermore, forcing players to do something is absolutely terrible design. If you have to introduce artificial limitations to ensure players play the game "right", then your entire design is faulty (which, right now, it admittedly is). Players should be incentivized to play all three rounds, not have to choose between punishments. FIX the coinflip... no more dry passing R1 as a rote strategy.
Engine decks like long rounds... however two cards is not a long round. The issue here is tempo. If you lose the coin flip and play a low tempo opener (e.g. an engine card), you risk your opponent going high tempo with their first two plays and passing for CA before you get a chance to gain value from your engines. So now if you run an engine deck, you also have to have a really consistent way to generate high tempo for when you lose the coin flip, which also means delaying and/or shortening your engine. And at that point... why not just go full tempo?
Tempo play is also highly incentivized because anyone able to generate a ton of points quickly now has the advantage of knowing their opponent can't pass their way out of the situation. Go first, play high tempo twice and pass... if their deck can't make up the gap in three plays, they go down a card. Go second, play high tempo twice... well, we all know how that ends.
I don't see any way in which this doesn't significantly hurt engines (and heavily promote tempo), unless coin flip is fixed. And if coin flip is fixed, we don't need to force anyone to play R1. Which is why the only explanation that makes sense to me is they're doing it to make it easier to port the game to mobile, once again at the expense of the game's core appeal.
I liked the idea of the initiative stat, where higher tempo leaders like Crach or Henselt would go first simply because they could play more points in a single turn vs low tempo leaders that had less immediate value when played like Foltest or Francesca. This is a great idea as usually the decks that can handle going first would now go first and low tempo decks that got more disadvantaged by the blue coin now wouldn’t be going second as often.
At the risk of veering off topic here, I personally LOATHE this solution to the coin flip, which unfortunately (for me) seems to be what they're leaning towards last I heard. What it does is fix leaders to specific archetype builds. Bran, for instance, has deck/archetype variants that are both extremely high tempo openers (e.g., Bran+Mork+Raider+WB) as well as insanely low tempo ones (e.g., Bran+QG+QG+Cerys). Where do you place him in the hierarchy? Place him too early in the order, and you make it impossible to run his low tempo variant. Place it too far back and his high tempo variant becomes incredibly oppressive.
This will also inevitably lead to tons of coin flip abuse. A major facet of deck design will be trying to figure out wombo combos on reactive leaders. And then CDPR will either need to change that leader's initiative (thereby killing any of their former archetypes/deck builds that didn't abuse this wombo combo), or constantly nerfing abusable cards. For instance, let's go back to pre-Cleaver Brouver. He'd probably be middle of the road to low initiative. Now introduce Cleaver. Well, obviously Brouver is now super super high initiative. However, once you've changed Brouver to match this high initiative... well, goodbye any Brouver deck NOT running Cleaver.
Ultimately, the only solution that works is one that awards Blue Coin some number of "buffer" points.
My personal vote has always been for a bid system (each player enters a blind bid following the mulligan phase, the highest bid then gives the other player an equivalent number of guaranteed points in exchange for going first). This allows dynamic shifts to accommodate the evolving meta, without having to constantly tinker with balance. It also heavily promotes skill based play as the better players get a feel for the optimal bids in various match-ups. The major downside is that it's potentially too complex for new players (would require a very well done tutorial explaining it). Vanitas has a good video exploring this solution, as well as making it more "new player friendly":
Swim's recent idea is pretty solid as well (~5 pt. "Roach" given to Blue Coin, only available R1, that allows a second action after, but vanishes after 3 rounds):
Essentially buys Blue Coin some temporary tempo to set up their engine, or escape a bad situation and get out of the round. This is an idea I hadn't considered before, and I think I like it though I'll have to consider it some more.