I, too, have keys on my vice, install it, snug down the nuts, and then indicate the fixed jaw. It's usually within .005, only needs tweaking.
I was also concerned with this issue. My solution is shown in post #3 of https://www.hobby-machinist.com/thr...25-rf-30-rf-31-mill-drills.38796/#post-332478On first look, I thought this looked like a good idea too, but I think I have to agree with Dave here. As I thought about it, I asked myself how wise is it to indicate via this jig, a machined surface on the column which may or may not be square to the table, when in fact all you really want to do is to square up to the table to begin with. I use the more traditional method of simple location keys on the bottom of the vice. However, if for some reason I were compelled to make an alignment jig of this nature, I'd do my locating on the table, not the column. In either case I think you can only hope to get it close and I would still run an indicator across the fixed jaw of the vice as I do now with the keys.
Found it in the rong fu thread http://www.hobby-machinist.com/threads/tool-for-quickly-setting-up-your-vice-on-the-mill.28527/