Why do some companies require leaving Thailand to apply for a Non-B visa while others allow transfers without leaving?

Okay, the real reason that some companies can get in country Non-B's for their employees and others can't is;

Many times companies cannot meet the documentation requirements INSIDE the country to get a Non-B from the immigration office because the requirements are far more stringent than they are at a thai consulate.

Also as was pointed out there is a time line where an employee needs to have so many days left on either a 30 day visa exempt entry or a 60 day tourist visa entry OR a 30 day extension off of one of those entries to do the in country conversion.

Bangkok requires 15 days left on your current stamp, Chiang Mai requires 21 days. If you don't have the days, you can't do the conversion

One last factor is SOME immigration offices can't do in country conversions at all and for those you always have to leave the country to get a Non-B from a thai consulate

I also believe there is a time line, 7 days? Which is not enough time for most companies to get the paperwork prepared.

a Lot of companies can/will not meet the requirements of the Immigration office. a Foreigner only gets the work permit if 4 Thais are named as employee in the company documents, but a Foreigner can only get the Non Immigrant B visa or Extensions of Stay if these 4 employees also get salary, pay their tax and get social security. If you have another job than teaching English language, you as foreigner also need a minimum salary.