Is there any reason I can't convert a 36/46 to a 36/52 chainring? My commuter bike is a converted cross bike (really just a cross bike with a rack on it).  It works great, but I occasionally wish I had a higher top end gear.  The crankset that came on it is a 36/46 cross gearing.  Is there any reason I can't just swap out the 46t chainring with a 52t?  It's all Ultegra 6800 stuff, and the cassette is an 11-32 cassette. I guess my biggest concern is that the chain might not be long enough if I ever cross-chain the 52t chainring and the 32t cog.
My guess is: since 50/34 and 11/32 works well, because it is commonly used, so should 52/36 and 11/32. Same tooth difference (16) between the front chainrings. Same total capacity (read further).

Take a look at this technical document
For Item 11 (inner chainring), it says Chainring 36T-MB for 46-36T/52-36T
For Item 12 (outer chainring), it says Chainring 52T-MB for 52-36T
I think you can conclude from that: 52-36 is supported by Shimano.

Now for the rear derailleur:
Ultegra RD-6800 comes in two cage lengths: short (RD-6800 SS) and long (RD-6800 GS)
Use this post as a guide to choose between the two.
Your total capacity becomes 32 - 11 + 52 - 36 = 37.
That's the maximum for the long cage.

Now about the chain:
This video illustrates perfectly how to determine the correct chain length. It shows that you need to use the inner chain ring and the smallest cog on the cassette (36-11). If you follow this rule, your chain length should be OK. Indeed the rear derailleur will be stretched even further than it already was in the other extreme (52-32).

Also an interesting read: Sheldon Brown's take on derailleurs