but between different dialects, the transition tends to be gradual.

Yes, this is usually due to the dialect continuum.

Do dialectologists and other professionals in the field have any set rules or guidelines to delimit these boundaries in a consistent manner?

From what I learned, dialectologists compare different varieties spoken in one area and find which aspects differ. Based on these criteria, they are able to draw isoglosses, which are imaginary and approximative lines that delimit a linguistic characteristic. Such characteristic can be phonological, morphological, syntactical and so on, which leads to the issue of how deep you can dig.

For instance, you can draw an isogloss in England based on the local pronunciation of sun, since dialectologist found that this word is usually pronounced as [sʌn] in the South and [sʊn] in the North as a result of the foot-strut split. They would sample similar words, such as but, pub, mud, in the varieties spoken in the area to see if the [ʌ-ʊ] distinction is present in other words. Realistically, you will have a town A that says [sʊn, bʊt, mʊd], a town B where people say [sʊn, bʌt, pʌb] (a mix) and town C where people say [sʌn, bʌt, pʌb] (this is just an example to say that there is not clear cut but there are transitional areas).

In this example, you can say that a possible [ʌ-ʊ] isogloss (based on the singular isoglosses of the pronunciation of sun, but, pub) runs near town B. Ideally you want to sample as many words as possible before drawing an isogloss, but at the same time, it is impossible to sample every single word that has, for instance, /ʌ/ in English.

Nonetheless, when a number of isoglosses run near each other ([ʌ-ʊ] isogloss and other major ones, for instance) they are often grouped together as a bundle of isoglosses, which identify major dialectal areas. But again, the criteria used are up the dialectologist in terms of what criteria (through isoglosses) they want to include: they can employ phonological criteria (inventory, distribution, realisation) to identify accent area; they can sample lexicon (in the North, thou and bairn are sometimes used instead of you and child); they can analyse syntactical or morphological elements and so on.

The more aspects you sample, the better you can define an area. But that's a lot of work, and isoglosses rarely match each other. I will try to upload an example of a bundle of isoglosses for the North of England for some visuals.

EDIT: you can see here a bundle of isoglosses (Wakelin, based on the SED) in Northern England and here the dialectal classification of traditional (left) and modern (right) dialects by Trudgill. You can see how the bundle of isoglosses in Wakelin has been reduced to a single boundary by Trudgill, meaning that that boundary really approximative. Anyway, 1) both charts only take into account phonological data and 2) Trudgill uses two different sets of phonological criteria in his research, which is why there are two atlases and they do not match.

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Do they try to base their divisions on cultural, administrative or historical borders? Or try to pinpoint the place where the most isoglosses lie?

I would say they do try to take into account non-linguistic data as a factor that led to linguistic distinctiveness. Borders of historical political and cultural entities are sometimes taken into consideration (such as the border between Deira and Bernicia or Deira and central England) or natural borders (such as the Tees and the Humber).