Things can get messed up when installing/uninstalling/reinstalling/updating drivers using the driver package, which in the case of the chipset and RST, neither are actually needed.
Firstly, the chipset "drivers" as some people call them are not even drivers. They are just a series of text files (.INF files) which tell the device manager that the chipset on the motherboard is an Intel one and that no driver is necessary. If you expand the system devices tab in device manager and double click (on mine it's) "Intel 8 Series/C220 series SMBus Controller - 8C22" and then click on driver details it will say no driver files have been loaded. If you don't install the chipset drivers on a fresh install your device manager will show an "SMBus Controller" with a yellow flag. The INF files rename this device to it's correct name and tells Windows it doesn't need a driver. Windows 10 will also download the INF file from Windows update for you.
As the chipset software package just extracts a load of INF files and puts them on your computer, you can actually find the extracted files and much more on the chipset here -
http://www.win-raid.com/t895f42-Intel-Chipset-Device-quot-Drivers-quot-INF-files.html
Form that link you'll see with X99 you're actually better off using chipset version v10.1.2.10 WHQL not 10.0.28 which is found on the Intel website. Intel doesn't appear to have updated the chipset software beyond 10.0.28 despite newer ones being out there.
With RST, Intel offers it primarily in 2 forms, an "f6 floppy" driver and the full package. If you don't use RAID, then you don't need the package. If you download the F6 form you just get the pure driver files. These can be installed in 2 ways, either during Windows installation by using the load driver module or post-installation by updating the MSAHCI driver directly within device manager and pointing it to the f6 floppy drivers.
Not all drivers can be managed purely through device manager but these two can and by doing so you remove unnecessary clutter from your PC and reduce the chance of problems elsewhere.
On a new install I will load the f6 Intel RST driver during installation of Windows and then post install I will manually update the "SMBus Controller" in device manager and point it to the pre-extracted INF files which I downloaded from the above link. It's a much cleaner end result and should eliminate the conflict you have had.