I am working on an Intel(R) Atom(TM) x5-Z8350 based hardware running a yocto embedded distrbution on it.

My first problem was that I was unable to access mmcblk devices in it. Following comments on https://github.com/coreos/bugs/issues/209 I was able to solve it by compiling a kernel with CONFIG_X86_INTEL_LPSS set.

But, when I run a kernel with CONFIG_X86_INTEL_LPSS flag set, xorg fails to install intel modesetting drivers (/usr/lib/xorg/modules/drivers/modesetting_drv.so) because it is unable to find drm device (/dev/dri/card0). As Intel specific drivers fail to load, xorg falls back to standard VESA drivers, losing hardware acceleration and RandR support.

I have tried linux 4.9.X, 5.0.X and 5.2.X on yocto warrior and yocto zeus distributions and I always get the same result: If CONFIG_X86_INTEL_LPSS flag is present, mmcblk devices appear, drm devices are absent and xorg is unable to start Intel drivers although i915 kernel video driver is loaded. If CONFIG_X86_INTEL_LPSS is not, set, mmcblk devices disappear, drm devices are recovered and xorg initializes successfully but no mmcblk devices are available.

Does anyone know about a relation between this two features? And, what is more important, does anyone know how to circumvent this and have both devices working at the same time?

I have a sucky Intel HD4000 card using i915, CONFIG_X86_INTEL_LPSS is not set, and mmcblk devices work. I have a Realtek RTS5129 sd card reader. I also have a micro sdcard --> usb adapter which plugs into a usb slot and becomes a /dev/sdx device.

I would check up on the INTEL_LPSS. Is it active throughout the system? Can you configure it? Otherwise, if it's only card readers the usb adapters or usb sticks beckon.

None of us have your board, I imagine so you're going to have to do the grunt work on your own. Pestering the manufacturer might yield something.

try to enable following kernel options
CONFIG_I2C_CHARDEV=y
CONFIG_I2C_DESIGNWARE_PLATFORM=m
CONFIG_I2C_DESIGNWARE_BAYTRAIL=y