A few decades ago, I used a Roland DXY-990 to plot artwork directly onto PCBs with great success. Even did a small production run of a commercial product that way. Here's a few things I learned:
Sharpies of that era worked well for etchant resist, but it seems they've changed their formula since then. Not sure if newer ones will work as well, because the newer ink seems much less durable. It's now easily washed off with simple alcohol, but it took something stronger back in those days.
I found that certain brands, and interestingly, certain colors of stock plotter pens worked better than Sharpies. The best were Staedtler fiber-tip. The red ink was the most durable resist, but left a broader stroke. The black ink did a finer stroke, but I had to be very careful during the etching process because it was much less durable.
I found that it's best to "rough up" the bare copper. I used fine steel-wool for that, but of course it left oil behind, so had to clean the copper thoroughly with acetone or alcohol before plotting.
In case you didn't notice it, the height of the plotter pens is adjustable. Loosen the screws of the holder and adjust up to give more clearance for PCB.