Ferment separately, then mix?

Brewed my first all-grain batch this weekend and ended up getting much better efficiency than expected, which resulted in 1.5 gallons more beer than planned. The extra amount meant I couldn't fit the entire batch in my 6.5 gallon carboy, so I opted for 3.5 gallons in one carboy, and 3 in another. I used the same yeast in both and the fermentations are proceeding very similarly.

I'm planning on mixing the two batches at bottling. I realize I'll lose more due to racking from two carboys, but I figured it would be better than putting 6.5 gallons in a 6.5 gallon carboy and losing a lot to blowoff. Is there any downside to doing it this way, or would it have been better to try to ferment all in one container?

You'll be fine! You could have filled one carboy, then kept the remainder for making starters or priming bottles.

Have some fun with it - dry hop one carboy so you can compare/contrast. Different yeasts would have been a good experiment as well, but it's too late this time.

SWMBO bought me an 8 gallon bucket fermenter for xmas. I love it since it can accommodate more wort if there is any excess and I don't have to worry about blow-off.