it's actually an issue the first time you do a run. As others have pointed out, you can just use a company. That tells you everything you need to know.
For about 150,000 baht, you could get 5 years worth of working visas in Cambodia, come and go as much as you want, no 90 day reports and very little time at immigration. Essentially, you could use that as your base and just travel to Thailand on tourist visas, if you wanted to.