Oh it was certainly esoteric and mystical most of the time. For instance, here's a quote from Paracelsus (A.E. Waite's translation), concerning the 'sun, light, darkness and night':

In the first treatise It was stated that the primal Iliaster was furnished with all the colours and with brightness and splendour all mingled together. From thence the four elements were secreted. Herein shall be stated in due succession what was added or subjected to the element of fire. In the beginning the first element, that is to say, the air, was extracted from the Iliaster, and afterwards the element of fire. From this a separation was made. First of all the white brightness was drawn out, and therefrom was made a material body, the sun. Therein is all the white brightness of the element of fire, and besides this is no white brightness at all in the whole element. The red transparency was also extracted and transferred to the stars, that is, to the moon and the other stars, which were distributed into many parts. While the white brightness was conglobated into one form, the red brightness was divided into many parts. Hence now follow day and night. For since all the white brightness was coagulated into one globe, it will be day wherever that globe is. Where that globe is not, there is no white brightness, but it is night and darkness ; for the red brightness transfers no light to the white brightness. Moreover, it must also be known that in the element of fire two natures exist, a warm and a cold one. Heat is universal in the white brightness, cold in the red. All fire which is warm is in the sun, and not in any element besides. All coldness is in the stars ; there is none in the sun. Hence it is clear that summer comes from the sun, winter and cold from the stars.

Reads a bit more like scripture than a strict inductive or deductive argument, doesn't it?

Alchemical writing was opaque and intentionally so. Jargon helped the alchemist appear smart and avoid questions. Basically; if you didn't understand, you simply weren't worthy to partake in the knowledge. Many alchemists were true believers but the opportunity for swindlers and scams was obvious, and there were always many of them. The Arab author Al-Jawbari warned of false alchemists already in the 13th century. In English literature, alchemist scammers were satirized all over the place; from Canterbury Tales in the late 14th century to Jonson's The Alchemist and Mercury Vindicated from the Alchemists in the 17th. But they were also frequently depicted as tragic fools following a vain folly. (see e.g. Greenberg, From Alchemy to Chemistry in Picture and Story)

So it was not entirely unlike today's esoteric movements (e.g. 'New Age') or yesterdays (e.g. Theosophy), in that there were both true believers and scams. And the New Age crowd, from Deepak Chopra to 'The Secret', have tried to sell their stuff by appealing to quantum physics. Unlike with alchemy though, in these cases they're not involved with the physics, and generally don't understand it either.

On the other hand, you have the interpretations of quantum physics that are close to the theory (e.g. Everett interpretation, Bohm interpretation) but have to be considered 'metaphysical' since they can't be tested. But that is the present-day perspective on it. Well after the Scientific Revolution and after alchemy had given way to chemistry, many scientists were still poor at distinguishing what they believed from what they could prove. Such as Dalton's atomic theory (A new system of chemical philosophy , 1808), which in its basic elements was correct and based on sound reasoning, but Dalton nevertheless went on to (for instance) make statements about the geometry of molecules which he didn't know nor could know. As late as 1844, Joule argued that vis viva (today: mechanical energy) could not be destroyed on religious grounds. ("the power to destroy belongs to the Creator alone")

So the interpretations of quantum physics now regarded as just that - interpretations and not physics itself - could've been considered actual physics 120 years or so earlier, long before you get all the way back to alchemy. (There are exceptions though; Lavoisier, who did more than anyone to expunge alchemy from chemistry, was for his day radical in his antipathy to metaphysics and instance on sticking closely to what could be shown experimentally)

Up to Lavosier throwing out the last remnants of alchemy, the more esoteric parts of the subject faded. e.g. Boyle in the mid 17th century was much less esoteric than Paracelsus had been in the 16th. The somewhat younger Nicolas Lémery was even more averse to it, and was for his day unusually uninterested in the Philosopher's Stone and such.

(All the while the alchemists were turning to chemists, many of them - like Georg Stahl - also studied medicine. But their medical theories showed comparatively little restraint. Old ideas like Humorism, with no scientific foundation, would still live on well into the 1800s)

So the short is that it's a bit complicated. Alchemy was esoteric and opaque, and regarded as such even by contemporaries, but it wasn't necessarily less evidence-based than contemporary ideas in medicine. Scientific rigor did not advance equally on all fronts at the same time. Simply viewing the metaphysical bits as an annex that could be removed from the whole wouldn't have occurred to them in the thinking prior to the scientific revolution. It defines the scientific revolution - an epistemic shift towards believing in empirical observation as the foundation of knowledge. But even the early practitioners of 'experimental philosophy' like Boyle were still very heavy on the 'philosophy' and drawing only lightly on the 'experimental' part.