He wanted a Chevy because it was the 'best'?
Well thats a matter of opinion!
What he wanted was FUNDING and if that came with an engine, even better. For the application (light weight body, small block race car) the Ford 289 was a much better choice than the HEAVY GM small block. An Olds engine, his 'real' first choice was incredibly heavy compared to just about anything else.
Of course Shelby didn't know the light Ford small block was 'coming soon'. Based on available engine choices say in 1959 the GM small block was a logical choice compared to what was available.
The GM small block weighs considerably more than the Ford engine, and weight is the 'holy grail' when it comes to racing!