Skipping the defatting stage in extraction of alkaloids I am attempting to extract certain alkaloids from green plant matter, which is very high in waxes and fats.

I understand that in this scenario it is common to first acidify and then use a non-polar solvent to de-fat the solution.

I am curious though: say I were to basicify and extract alkaloids without any de-fatting. If I were then to add HCl solution to the non-polar solvent which now contains the alkaloids, wouldn't this in theory be equivalent to the de-fatting stage? Wouldn't the alkaloids would now be in the aqueous layer, and the lipids would be stuck in the non-polar layer?

As the acid/base method is so common, I am wondering if there are any downsides to the method described above that I am unaware of. I only have enough material for one shot so I would just like to hear some input before I attempt this expedited method. 

May main fear would be emulsions that wouldn't break up. Is this a valid concern that is remedied by a preliminary de-fatting stage? Are there other concerns I should be wary of?
One big risk with the method you propose is foaming and gellation turning your extractions into a huge mess.  Under basic conditions, the fats (e.g. triacylglycerols or TAGs) are likely to hydrolyze, forming carboxylate salts of fatty acids.  "Carboxylate salts of fatty acids" is a long way of saying soap.  These soap-like compounds could lead to excessive foaming or gellation of the sample, which will hinder phase separation and gunk up your apparatus.