Most of this stuff is dependent on on the board vendor.
Some makers don't want you to squeeze more than one board into a single file. Some will allow you to make an array of images in the file and make a single board that gets chopped up (this is called panelization). Others will do the array for you from a single file. For small boards, they're probably squeezing them into the slack space on other people's orders.
Some makers only have green soldermask. It's specified as part of the order if it's variable.
.062" boards are pretty common. Is the thickness critical (like on a card edge connector, where it has to interface with the slot correctly)? This is also specified as part of the order.
As for pulling outlines from the mask layers, is there any reason that the outline on one layer would be different than the outline on the other?
