I've played a lot of incrementals on mobile, and thought I'd list how a few of them tackled this issue. Realm Grinder and Cells to Singularity did a similar thing, where they have dynamic orientation, meaning on mobile you could do either landscape or portrait, whichever you prefer. They both started on PC though and then ported to mobile, and when they did so they ported their existing UI and made a second UI especially for mobile.
Another couple are Time Clickers and Zombidle. They feature crossplay (which is a fantastic feature to have for a game with multiple platforms by the by) and both have the same UI on mobile and PC, landscape. Time Clickers started on PC but zombidle was developed with cross-platform play in mind.
Merchant's method is option 2. Mobile landscape and PC landscape. And yeah it's perfectly playable, but it just doesn't feel like it fits.
There's another consideration for interactability. If the game has a lot of stuff to interact with on the screen like with Time Clickers where active play is shooting blocks, then a landscape format tends to work better. Portrait is fine for games like cells, adventure capitalist, or realm grinder where the overwhelming majority of gameplay is tapping buttons to buy buildings, but for games with more active elements, landscape just gives more real-estate. There's more room for those active elements and the UI. More information can be presented since word wrap isn't as big of a concern The more active the game is, the more sense landscape makes over portrait.An example of this is Shark Jump's Melon Clicker where to increase your income you need to manually clear obstacles and plant new melons. It needs to be in landscape because it's such an active game. And since we're to be managing crops, landscape would probably be better.
As for my personal preference, I tend to play more inactive incrementals like cells to singularity or eggs inc over more active ones. For inactive incrementals, I like portrait better. I'm usually focusing on something else like a youtube video or it's a loading screen in a game, or something like that. Single-hand play is very useful for that sort of thing.