I suggest you just leave it as is - for a while. Get the machine cleaned up, fix the little things that need attention, service it and get it running. Find out what the issues are: some you can see, some only show up after you have used it for a while. The actual step in the table looks like it would be pretty easy to work around (sure, a bit of an annoyance - but most old machines will have some unique character, working with the issues is called "machining").
I find I use some sort of a table attachment about 75% of the time (vise, rotary table, dividing head - what ever), and so you can simply dial in your reference planes. You already know you'll need to add a shim. When task involves bolting directly to the table, you may be able to avoid the step, shim the component, use a sub plate, . . . . lots of options.
If everything is working out well for you, and you really enjoy the machine - then of course, fix the table surface. My advise is that you don't start with that, run it for a while first.