Btw, thanks a lot. Your responses help me out to know what can be the issues.
It would be good to know why uart3 didn't work :-(

You can use the same timer for different motors as long as a different channel is used. If you look at the default configuration for that FC (below) you will see that MOTOR 1 & MOTOR 2 both use TIM3 but they use different channels of that timer. Likewise with MOTOR 3 & MOTOR 4 which both use TIM2 but with different channels. It's a combination of the timer and channel that makes it unique (the same as it is with stream and channel for the DMA). So there must have been some other internal conflict going on, or a bug in Betaflight with the timer combinations being used. It's a bit frustrating having to use trial and error to get things working when figuring out the solution should be logical.

Quote:resource MOTOR 1 B00
resource MOTOR 2 B01
resource MOTOR 3 A03
resource MOTOR 4 A02

timer B00 AF2
# pin B00: TIM3 CH3 (AF2)
timer B01 AF2
# pin B01: TIM3 CH4 (AF2)
timer A03 AF1
# pin A03: TIM2 CH4 (AF1)
timer A02 AF1
# pin A02: TIM2 CH3 (AF1)

True. We all know how software works. There is always a bug or sth odd there and we don't know it :-)