As "tragic" Whitney Houston would have said, "It's not right, but it's OK..."
Notches make the timber more susceptible to shearing at the notch, but as it's only a pergola it should be OK...as long as you don't get people jumping up and hanging from the joist near the joint.
As Woody said, it's better to rest the timbers on a single, full length timber securely bolted to the wall.
Thank you gents. I was going to notch it as I thought it may look better but I think I will rest it on a single piece of timber as you suggest - less work for me also.
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