Hi Ian,
I use methylated alcohol (MA) because it is inert to metal and plastic in the hoses and have cleaning properties.
Usually, when running it in the brake system I will action the brakes a few times to move the pistons and help cleaning.
The use is not intended to have any hydraulic capacity. If was to be used as such the water content will become a problem so it must be ensured that is not subject to high pressure as it would occur in a closed system. But this is not a problem is used only to flush the system.
The only caution needed is to make sure clear brake fluid is running through the purge valve replacing the MA, because the alcohol is purple it is easy to spot. and that the operation is done without interruption. Having said that if the MA is left for a couple hours "soaking" the system this poses no issues.
I've done it on all my bikes, mostly because all of them are Honda with CBS, I have used it also in my cars and never had any problems.
I service my calipers every 2 or 3 years depending on mileage and never found any sign that MA would be an issue.
I know people usually just push new fluid on used and make a direct replacement but my opinion is that brake fluid have no cleaning capacity and the direct replacement doesn't remove the surface coating the used fluid will deposit throughout the years.