If toxicity is related to the charge of the compound and to the solubility of it, my guess is that it will be different. Nonetheless, what matters at the end is the final pH of whatever you are using to test cytotoxicity.
Thank you! I also agree, that the solubility could matter, as dox base is practically insoluble in water. It could interact with serum in medium, then the concentration of free drug could be lower compared with dox HCl.