There's no right or wrong with that watering deal, I don't water my OD photo's to much run-off, but then I use fairly low hardness ppm water, monitor and adjust pH going if needed, and test in-pot pH weekly at least,... also feed on the milder side, more often, and sometime with organic nutes... It also is going to depend on the soil's water holding properties, and how root bound things are... flushing isn't always a bad idea, but one concern is if it stays water logged for long, smothering roots O2 uptake, promoting fungal/rot issues,... So IMO, unless there's a real need, like really off pH, obvious nute burn/overfeeding, I don't do flushing... Some folks would not agree with this though, they feel a real flush once at transition or early bloom is smart, unless it's all organic based... typically, a flush is 2-3+ x pot volume of water, with regular checks of pH and ppm's on run-off to see how its working,...
As for the soil pH probe, no significant root damage is done by using that; this is why I like the Accurate 8 unit, vs. a "pro" model that is actually a type of bulb electrode device the same as pH meters (liquid only),... one less fussy device to care for and service, and much less expensive too,...
That run-off value is pretty high, but with such a small amount indeed it's not a solid indicator,... ease up on the ppm input, both those are fine, but I'd get some K in there too at this late stage,..
