Move miscellaneous defines to data driven

[fauxpark]

Description

Moved a bunch of defines with too few instances to warrant separate PRs:
LEADER_TIMEOUT -> leader_key.timeout
LEADER_PER_KEY_TIMING -> leader_key.timing
RGB_MATRIX_TIMEOUT -> rgb_matrix.timeout
MATRIX_IO_DELAY -> matrix_pins.io_delay

Moved defines that were missed (indicators, encoders, matrix, ws2812, polling interval)

Removed some pointless code:
Commented DIODE_DIRECTION in custom matrix boards
LED_PIN_ON_STATE 1 in .c

Types of Changes

• Core
• Bugfix
• New feature
• Enhancement/optimization
• Keyboard (addition or update)
• Keymap/layout/userspace (addition or update)
• Documentation

Issues Fixed or Closed by This PR

Checklist

• My code follows the code style of this project: C, Python
• I have read the PR Checklist document and have made the appropriate changes.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• I have tested the changes and verified that they work and don't break anything (as well as I can manage).

[fauxpark]

Only two SHA mismatches are ash1800 and ash_xiix, as expected.