Account currency on IBKR doesn’t matter much. It’s just used for reporting, some minor odd charges here and there, and for converting negligible cash leftovers to. For all other purposes they keep track of your balance in each currency separately and converting between them requires you to do an explicit trade to do so.
If you have CHF in your bank, you should just transfer it as CHF to IBKR and exchange there, the transfer is free and you get unbeatable currency fx rates.
If you transfer USD, then it’s no surprise a good chunk of your cash will disappear between different intermediate banks and horrible fx rates all banks charge.
Vanguard’s US ETFs are more profitable because of lower management fees and ability to reclaim US withholding on your swiss taxes. Not because of the currency. Aside from trading formalities, you’re buying exact same basket of stocks, it doesn’t matter if the price is quoted to you in franks, dollars, euros, etc… Once the trade is done your cash is gone and you have your basket of stocks instead - much more important is what’s inside of it.