Good morning, working my first PCB designs in an EDA (I’ve been working around hardware electronics for years) excuse my lack of experience on these “new fangled tools” 
I’m looking for some guidance on the PCB layout and export.
I have a prototype design involving a mixture of microcontroller, TTL and OPTO (not SMD), It is a relatively “simple” 2 sided PCB 4 x 6" and a ground plane. I figured this was a good point to dip my toe in EDA. I have included three Molex RJ45 pcb mount connectors for some convenient I/O connection.
I am at a point where I’m sharing Gerbers with PCB services. Ideally, I would like to use an automated “no touch” type service to allow me flexibility in work hours. An issue I’m running into is no matter how I define holes they always seem to be seen as PTH when I upload to the “touch free” PCB vendors. When I pour the ground plane the locating holes for the RJ45 connector plastic pins (just need to be simple holes), the pour goes very close to these. The vendors see this as “too close to plated through hole” and kick back the design. Another issue with one service they didn’t accept the .XLN files, but recognized the .Drill files when I downloaded the NC Drill (Excellon) and rolled those into the Gerber folder (rather than the .XLN). What is the difference between the .XLN and the .DRILL?
So close now