Hi Eishi SHIBUSAWA,
I have confirmed it for you that, the default version BSP Linux L4.1.15_1.1.0 on the MCIMX6DL-SDP boot up is more than 5 second. The behavior in your side is normal. About how to shut down the board less than 5 second your customer need to to modify the u-boot and kernel themselves, we do not have this sulution for it.
Here I can give you some recommend and reference thread, you customer also can try to Remove the uboot bootloader and use whoosh simple booter for imx6,For the kernel remove any option that is not used in your application, the smaller the better. Also when dealing with the RFS not all the systems have the same mount time.Details you can see in the following thread. Hope them can do help for you.
Linux Fast Boot on i.MX6 Sabresd Board
Booting i.MX6 under one second - i.MXDev Blog
https://community.nxp.com/message/895274?commentID=895274#comment-895274
Have a great day,
Rita
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