I used this calculator with the inputs 48V and 4A to be on the safe side. It says that the required track clearance is 0.83mm.
Would something like this
http://www.digikey.com/product-detail/en/64P44WE/V1042-ND/38933 be suitable? This particular board has no plating.
Your call... You will have to use jumper wire on the underside of the board to connect everything... or you can look into 'wire wrapping', which I think is actually a very cool skill to have...
Anyway, I should mention that something like this :
http://www.digikey.com/product-detail/en/8015/V2009-ND/415998
May be suitable depending on the layout of your board.
The hole spacing is roughly 2.5mm, with 0.5mm clear between each pad. Now, this is below the calculated value you noted, but there are a couple tricks you can use.
First, the calculator you used will give you excessive values to be on the safe side, so you have a little wiggle room.
Secondly... if the gap between the pads is 0.5mm, and you need more, simply leave a row or two of unused pads between the +48V wires/traces and the Ground wires/traces.
Remember that as soon as you lower the voltage, you no longer need the spacing.
Additionally, if you are concerned with the thickness of the copper pads, you can simply double the width to compensate. So instead of using one row for the 'high' amperage current path, use two. They can be two separate paths, but it would be best to put the paths side by side and actually tie them together.
Now... The voltage you are using and the current you are using isn't technically called 'high', you will find that you will need to carefully plan your circuit. Linear regulators will get very very hot, and the higher current path(s) can always be reinforced by laying a small piece of wire along the path and soldering to that instead of relying on just the solder to join the little pads together.
So.. while I gave you a calculator to see what happens with the numbers, I would also discourage the need to go to a bunch of special steps to order special board requiring unique construction methods.
Let us know what you think, and if you are willing to share the schematic, we can help out more.