arm9select is just a chain-loader, it mainly resides in the distributed arm9loaderhax.bin, while relying on
FIX94's arm9loaderhax fork for the backlight value on boot.
You have to know the following:
• You cannot update FIX94's arm9loaderhax fork since it was never actually updated (last change was 4 months ago)
• You cannot update arm9select since last release was 4 months ago
If you don't want to update those but rather install what's called "A9LH v2" (i.e. Aurora Wright's updated fork), you just have to follow
that part of the guide.
After installing that, you probably won't be able to use arm9select, but you can still chain-load stuff when using Luma3DS.
If you don't like the screen flashing, you can:
1- Install the no-screeninit version
2- Wait for a new release of Aurora Wright's fork, which will include both screeninit and no-screeninit (you can switch between the two by renaming the arm9loaderhax.bin file), and also offers the ability to boot without an SD card.
(If you don't want to wait for an official new release, you can find precompiled versions of that,
here for instance.)
In any case, when installing A9LH v2, make sure that you are using
the latest version of SafeA9LHInstaller (v2.0.3 at this time), and the right input files (data_input_v2.zip on Plailect's guide).