I guess that may be rather hard for @trevanian to do @bhuvanchandra.dv as he can’t seem to enter the U-Boot console any longer even though at least our regular BSPs do define CONFIG_ZERO_BOOTDELAY_CHECK which means that even when setting bootdelay to zero one should still be able to stop U-Boot from auto booting by sending any character via serial terminal connected to it.
However maybe the issue at hand is a quite different one and I do suspect it might have to do with UART RX/TX having been swapped in later hardware revisions which this proprietary Boot2Qt stuff might still not quite handle properly.
Could you tell us what exact hardware model/revision of an Apalis iMX6 you have? Do you actually get any UART output at all now when booting?