Here's an idea. Instead of having all of these workarounds like phantom runners and minimum batters faced, get to the heart of the problem. Put roster limitations on pitchers. The 1993 team had 16 pitchers on the roster all year. Just past half way through the year, the Jays have already had 31 pitchers. I know it's a bit of an outlier with injuries. But 2016, which was the absolute poster child of starting pitcher health, had 27.
All of these problems that are in baseball right now revolve around teams manipulating dozens of jobber relievers who might be released by the time they hit arbitration, but can average 10K/9 at max effort in short bursts and minimal workload. Put a hard cap of 20 pitchers on each roster for the year. A team hits that cap and gets an injury? Too bad, you're putting your shortstop on the mound. Should have planned things out better. This will incentivize teams to balance velocity and performance with longevity. Every reliever in the pen should be reasonably expected to carry 70-100 innings in a year. Forcing every team (except the ones with ACTUAL good pens, not just manipulating garbage) to carry 3 relievers that average a 4.50 ERA over 250 combined innings will help end extra inning games faster.