I know what I usually have to do but I don't know how that works with you or the other inexpensive online fab services.
I use Easy-PCB which is basically the same as Pulsonix. Not freeware. I generate a set of Gerber files for copper and resist and silk. I generate an Excellon drill file (for plated) and another Gerber with just the outline. I can also generate an Excellon file for the outline. I don't ever give anybody my actual design files.
If I include plated slots in a part, they show up as 'route' commands in the excellon plated drill file. I usually use a unique size for the slot tool. My PCB package lets me do that. Then the Excellon file has defined tools for drilling and another tool that gets used for routing. I tell my PCB vendor via email that Tool T04 is supposed to be a router bit, not a drill. Then they can load a router bit. If I want unplated slots or internal routes, that data goes in a separate Excellon file for unplated.
This usually gets communicated via email with my vendors. Given that I can't do that with your fab, can I do plated slots without it being a guessing game to see whether they looked at the drill file and spotted the route commands? I'd rather know definitely whether I can or can't do slots reliably. I don't do overlapping holes. Most places will bounce that anyway.
This is mostly for ham radio and other personal stuff so I'd rather use a $10 fab instead of a $250 fab.
Thanks.