I agree, it depends a lot on how they implement loot boxes (if they implement them). Loot boxes are not inherently a bad thing.
I disagree. Microtransactions (loot boxes, whatever you want to call it) always warp
design decisions. This is a mostly non-controversial point. Once you include microtransactions, you want people to buy them. Therefore you'll make game design decisions that exist to do THAT rather than providing better gameplay. It's hard to think of any case where if (as a designer) you were purely interested in providing your ideal game experience but you would also want microtransactions. I don't personally like Jonathan Blow very much, but I think the following talk is insightful on this particular topic:
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A too-brief summary: he lays out an analogy to the monetary incentives of early television (syndication, needs to be able to air multiple times and without context, needs to be regularly interrupted by ads, etc) and the way those warped choices (in the analogy, it's harder to make contiguous plot arcs like HBO prestige television, etc). This doesn't mean the end product is ex ante bad - just warped to be worse than if those incentives weren't there.
Of course, you've accurately pointed out that this does also apply to Magic! It's absolutely true! I personally vastly prefer the expansions model of Netrunner. And clearly the booster pack commercial model does affect design in unfortunate ways - see for example God-Eternal Oketra in limited, incentives in mythic/rare design regardless of the quality of the resulting constructed format, etc.
