Welcome to the community @topgummy
You are correct. if a new contact abandons checkout after entering their email address AND opts-in to marketing, they will trigger and enter both your welcome flow and your abandoned checkout flow (subject to any filters you may have for those flows and ecomm integration is set-up to push opt-ins to your welcome flow list).
How I approach this to ensure they are not receiving cross-flow emails is to consider the Welcome flow as the primary on-boarding to purchase CTA. The welcome flow is typically where you offer your introductory discount so you want to encourage them to purchase, or at least start their purchasing journey by entering the checkout.
With that in mind, the first email in the Welcome flow is sent to ALL contacts who subscribe (opt-in) as that confirms their optin/offers the discount and some 'why buy from us' messaging. I then add filters on the subsquent Welcome flow emails themselves to exclude contacts who have started checkout or have purchased since entering the Welcome flow. Those 2+ welcome flow emails are usually a combination of unredeemed discount reminders, brand values, info-guides etc with the objective to drive them to checkout/purchase
That approach means that if they start checkout (as in your example), they effectively 'exit' the welcome flow after the first email and receive my abandoned checkout flow emails (which includes a discount call-out if unredeemed). Similarly, if they purchase, they stop receiving the checkout abandon emails and start receiving the post-purchase flow emails.
Alternatively, if you want a subscriber to your list to receive some of your welcome flow emails even if they checkout/purchase, you could just enable smart send on those 2+ emails. That way, you won't be hitting them with a 2+ welcome flow email if they have received an abandon checkout email (or any other email) that's been sent to them within the past 16 hours (smart-send default window).
Does that help?
Regards
Andy