shopify markets - com and eu

Hi all! So I have a dilemma with international markets. I do have an .eu website which is in English and is meant for EU english speaking customers. However, I also have an old .com website which I didn't develop for quite some time as I was busy with .eu. But now - the time has come and I want to ask something about Shopify markets and SEO. As you may know - Shopify allows to have multi-market shop within one admin, allowing an easier and more streamlined administration of the shops. However, I would like to keep .com shop separate at least for now as it has different payment providers, currency, and the fulfillment chain is a little different. But the problem is that both websites would have practically identical content as it's still the same products. Do you see this as a problem, and how can we solve this? I've read that we can help google robots understand that the .com is only for US by having USD currency, mentioning FREE US SHIPPING etc... and also add both websites in the footer of each website. But what else can we do to start everything correctly?