Japanese vs Other Region accounts: You do need separate accounts to buy from both their Japanese store and a non-Japanese region store. There is a feature to combine logins, but the intended use is to combine two or more separate logins from one region. (I combined a US account and a Japanese account and after a while that ultimately broke my ability to buy anything from the US store until I contacted support and it took a while for them to fix it and get my accounts unlinked again.)
You can easily log out of one account and into another on the Kobo app or desktop software, but you lose all your downloads, and have to redownload them again when you log back in to the prior account.
VPN: I am in the US, and I do not need a VPN.
Forwarding address: You do need a Japanese address and phone number. I used a random Japanese web site that generates real-looking fake addresses and phone numbers and have been able to use the service without any issues. Your experience and results may vary. Buyer beware.
Japanese credit card: I don’t own a credit card, but I do have a debit card that can be used on MasterCard’s system. It works for me just fine with Kobo. (For reference: My debit card works with Nintendo’s Japanese 3DS eshop, but does not work with Nintendo’s Japanese Switch eshop.) My credit union has a (very small) international fee tacked on to my Japanese Kobo purchases.
File format: Kobo uses EPUB format. However, files are saved as DRM’d “KEPUB” format. I use a program I bought for $50 that strips the DRM from any Kobo books I download into the Kobo Windows desktop application. It’s possible Callibre can handle this, but I couldn’t get it working.