What you need to remember when freefalling is that is it a lot harder to bring your boat from being over vertical than it is to push your bow down to become more vertical. It is possible to kick the nose up to correct yourself from falling over the handle bars but you must avoid landing in a sitting upright position which will expose your spine to impact injuries. In certain situations you may be able to use the back blade of your paddle to pry the bow back up from being over vertical but this is dependent on the drop you are running and it is a very tricky technique.
You will have much less control over your boat when in a freefall scenario than you will when bow stalling etc.
My advice to you when it comes to controlling your freefall is to decide before running the drop how you want to land and to run the waterfall in such a way that you are being active rather than reactionary i.e if you want to land vertically then roll of the lip, spot your landing, keep your weight moving forward on tuck for impact - rather than flying off the lip in a boof and trying to kick your heels down at the lust minute (although this is a good way to avoid an unwanted flat landing!)
And like you say, whether or not you are boofing or plugging - always land with your body tucked forward so that your core muscles, rather than your spine, take the brunt of the impact.
Hope this helps.