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When you blend different architectures you WILL get contextual tag collisions (e.g: canonical tags don't work the same across both architectures, or Meta robots tags, or hreflangs). What you are suggesting is probably the best thing you can do, I stand behind WordPress quite firmly, even when it's used to augment another CMS (instead of replacing it). That being said, if you believe you are going to be able to predict all the issues which arise in advance - think again! Do your best on that front (obviously) but you need to manage your client's expectations. There is going to be some fallout. There is going to be analysis needed. There is going to be dev work needed to create a seamless integration. It's good that you're being diligent and trying to predict everything, but with the complexities of the modern web (the same thing can be coded in thousands of different ways) you really need to accept there will be some problems that will need fixing. You'll need to hold some budget back for that stuff, or you'll be up a gum tree