How can I get or create a reference genome for Bacteria?
How can I get a reference sequence for other strains of E. coli?

You can use any sequence you want as reference for a variation analysis. It just depends on the question you want to answer.
So to keep it simple, your Question is:
What are the variant region from a fresh sequenced E. coli K12 sample?
To know the differences from your known strain E. coli K12. A reason for this could be that you work with the strain K12 through out several years. During your studies you changed the conditions for the bacteria, like adding antibiotics or change the growth media. So some of the E. coli would adapt to the antibiotic and become resistant to it or they adapt better to the new media. This happens because some nucleotide changed. With each new experiment you used the best adapted colonies from the previouse one.
So you sequence your bacteria and compare it with the E. coli K12 strain. In this case this is your reference. If you use another strain, like SE15 or SE11, as reference, your result would not give you any answer for your question.
If your used data and publications gives you the information which strain were used, then use the given strain as reference.