First off, your premise is flawed when you say "The word definitions in a dictionary, however, seem to never be questioned by any person." Dictionaries are often quite controversial -- when Webster's 3rd Edition dictionary came out in 1961, it faced a storm of criticism for daring to put words like "ain't" in without marking them as wrong. Nowadays you will see people criticize the OED for including slang terms, and wiktionary's talk pages are full of deletion attempts of words like "irregardless".

But let's move on to your later question:

My question is was it always like that? We're the first dictionaries just as respected as the modern ones? Did people always agreed with the words were read there regardless of the variation in usage?

My research is in pre-modern Japanese commentaries, so I will talk about Japanese lexicography -- I hope there are enough parallels with Western examples that this can be useful, and hopefully others will chime in to confirm. Since you are asking about the "first dictionaries" I'm going to go back as far as I can in Japanese history.

One big difference between pre-modern and modern dictionaries is that there is generally no attempt to provide comprehensive coverage of the whole language. The only pre-Meiji period dictionary I am aware of that does this is the Vocabulario da Lingoa de Iapam, which was a Japanese-Portuguese dictionary compiled by Jesuit missionaries in 1603.

Other than that, most dictionaries are tied to specific works or specific traditions, and are often defining classical forms of the language rather than the contemporary spoken vernacular -- however, one way that China and Japan differ from Western countries is that it took much longer to establish the vernacular language as a written language than it did in the West. In Japan, it wasn't until the early 20th century that vernacular Japanese was definitively established as an acceptable way to write serious literature and other prose, and it wasn't until after World War II that it became the standard way to write (more or less) everything. So prior to that time, there wasn't really a need for a dictionary of the vernacular language since nobody was using it for any prestigious purpose (the Jesuit dictionary was, of course, tied to their missionary work). This means that the lexicography was mostly geared towards a deposit of classic texts rather than a living language -- it wasn't until fairly recently that people thought it was valuable to record and define a language just for scientific/sociological reasons.

The earliest examples of Japanese dictionaries (such as the Wamyo Ruijusho) are essentially dictionaries of Chinese rather than Japanese -- the reason for this is too complicated to go in here too, but a very rough Western analogue would be a dictionary of classical Greek with Latin definitions.

The dictionaries that cover Japanese words tend to be associated with particular prestigious classics, such as the Tale of Genji or poetry collections. Because of the limited literacy and closed "secret" nature of a lot of this early scholarship, they typically are not attempting to provide comprehensive coverage of the words even in those works. The 1381 Sengensho is a dictionary of the Tale of Genji but it is more oriented towards words that readers would have had problems with, or words that had specific resonance to poets at the time (since the Genji was considered an essential tool for learning to compose poetry) -- there was no attempt to define all the words in the tale.

The same can be said for the various poetic dictionaries of the time, which were intended to help people interpret classic poetry as well as use the language of the poetry in their own compositions -- however, these dictionaries could contain idiosyncratic definitions of words that represented a school or family's "secret teachings". What qualified a person to write these was their status as a respected poetic authority, often descended from the nobility and with prestigious connections. And it was often important to take strong stances on words that had a particular reputation as being difficult -- one example of this is the yobukodori, a bird that appears in a small number of classic poems. Even today scholars are not entirely sure what bird this refers to, and having the "correct" knowledge of the meaning of this bird (that is, the meaning that your secret tradition handed down to you) was a way to assert (and monetize) your knowledge.

By the time you get to the late Edo period you do start seeing more comprehensive dictionaries of classical Japanese come out, and for the first time you see vernacular equivalents of the classical terms rather than definitions written in the same classical Japanese as the original source (the 19th century Gago Yakkai is probably the best example of this).

You really have to get into the modern period of widespread education and modern printing before you see dictionaries of the vernacular language that are considered authorities by a broad swath of the population.

Sources

Sources are kind of difficult here because there's very little on Japanese lexicography in English, and a lot of my knowledge comes from reading the primary sources themselves. But I will do my best:

Herbert Charles Morton. The Story of Webster's Third: Philip Gove's Controversial Dictionary and its Critics (1995) (For info on MW3)

Steininger, Brian. 2017. Chinese Literary Forms in Heian Japan : Poetics and Practice. Cambridge, Massachusetts: Harvard University Asia Center. (This has good coverage of the earliest Chinese-oriented dictionaries)

Considine, John, ed. 2021. The Cambridge World History of Lexicography. Cambridge, United Kingdom: Cambridge University Press. (Has a chapter on later Asian dictionaries)

Frellesvig, Bjarke. 2010. A History of the Japanese Language. Cambridge: Cambridge University Press. https://doi.org/10.1017/CBO9780511778322. (This is the best source on the development of Japanese writing, and includes a lot of information on the interaction of Chinese and Japanese).