Part disappears when touched, but is not pass-throughable. What am I doing wrong?

The problem is the value is going above when, while your script is checking if it EQUALS one. Here's a fixed version of your code:

local touchedpart = script.Parent

function onTouch(part)
    while true do
        wait(0.3)
        local tptrans = touchedpart.Transparency
        touchedpart.Transparency = tptrans + 0.12
    end
end

touchedpart.Touched:connect(onTouch)

if touchedpart.Transparency >= 1 then
    touchedpart.CanCollide = false
end

It also should noted that you're only checking once for the Transparency. Here's another version of your code that should work better:

function onTouch(part)
    while true do
        wait(0.3)
        local tptrans = touchedpart.Transparency
        touchedpart.Transparency = tptrans + 0.12
	if touchedpart.Transparency >= 1 then
	    touchedpart.CanCollide = false
	end
    end
end

touchedpart.Touched:connect(onTouch)