Fix a handful of CLI errors

[fauxpark]

Description

⚠ frobiac/redtilt: Layout "LAYOUT" is offset on Y axis by 1
⚠ skme/zeno: Layout "LAYOUT_default" is offset on Y axis by 0.235

⚠ handwired/tractyl_manuform/5x6_right/arduinomicro: DIODE_DIRECTION in config.h is overwriting diode_direction in info.json
⚠ handwired/tractyl_manuform/5x6_right/elite_c: DIODE_DIRECTION in config.h is overwriting diode_direction in info.json
⚠ handwired/tractyl_manuform/5x6_right/f303: DIODE_DIRECTION in config.h is overwriting diode_direction in info.json
⚠ handwired/tractyl_manuform/5x6_right/f411: DIODE_DIRECTION in config.h is overwriting diode_direction in info.json
⚠ handwired/tractyl_manuform/5x6_right/teensy2pp: DIODE_DIRECTION in config.h is overwriting diode_direction in info.json
⚠ maple_computing/ivy/rev1: DIODE_DIRECTION in config.h is overwriting diode_direction in info.json
⚠ maple_computing/launchpad/rev1: DIODE_DIRECTION in config.h is overwriting diode_direction in info.json
⚠ nightly_boards/n40_o: DIODE_DIRECTION in config.h is overwriting diode_direction in info.json

⚠ lfkeyboards/lfk78/revj: Matrix pins are specified in both info.json and config.h, the config.h values win.

⚠ lily58/r2g: SPLIT_KEYBOARD in rules.mk is overwriting split.enabled in info.json
⚠ lily58/r2g: Feature bootmagic is specified in both info.json and rules.mk, the rules.mk value wins.
⚠ lily58/r2g: Feature oled is specified in both info.json and rules.mk, the rules.mk value wins.
⚠ splitkb/kyria/rev1/proton_c: LTO_ENABLE in rules.mk is overwriting build.lto in info.json
⚠ splitkb/kyria/rev2/proton_c: LTO_ENABLE in rules.mk is overwriting build.lto in info.json

And fixed some duplicate key errors in wt60_h1 and _h3 blocking API update.

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).