I think it completely depends on model. I don't know how HTC does it (never owned an HTC before), but Moto phones have "battery stats" files. Maybe it's an overall Android thing. Again, I don't know. I've never messed with AOSP or anything.
However, my DX has a battery statistics file. It's main objective is to increase the accuracy of the phone's battery. It runs off of the highest max charge, lowest discharge before the phone shut off principle. And we have to "recalibrate" it whenever we do major upgrades to the ROM. We recalibrate it by deleting the stats file and doing a discharge/charge cycle from 100% to 5% back to 100% while off. If this file is not calibrated, battery reporting accuracy goes in the toilet. And seeing how Android will shut down the phone if it reaches that certain percent (5% for the DX), even if the battery really has 30% left, it works like it's dead.
But the difference to know here is that it's the OS that is controlling it. So if Android thinks that the battery is 100%, it shuts down the charging circuit, period. Even if you turn off the phone and hook up the charger. Android boots up a low-level version of itself to facilitate the charging. Don't believe me? Go to the DX forums and look at threads where people say they were installing ROMs, screwed up, tried to SBF (flash it back to stock), but couldn't because their battery was too low/dead. Then they tried to charge it, and it doesn't charge, even when powered down. Because the OS is corrupt.
So, unless HTC has something hard-coded into their phones to allow them to charge without any software, leaving the phone off and charging it beyond the point where Android says it's enough is shenanigans. Maybe Seido does put those cards with their batteries. Personally, I think it's a CYA maneuver that is left over from the old days where it was applicable.
Edit: Another thing. Yes, fully discharging a Li-Ion battery is bad. But the detail to make is that it literally means a 100% discharge. Cell phones do not allow that.