All interlinears will be aligned to one language or another. Sometimes you can find the same language pair aligned both directions. For example here is Genesis 1:1 (ESV) with Hebrew interlinear:
Obviously the word order there follows the English translation. The chunks of Hebrew are shuffled around to be under where the equivalent bit of English is. Here is the same Hebrew text with English added as an interlinear:
This follows the Hebrew word order (note this segment of Hebrew starts on the right!) and shuffles around the bits of translation to be under the Hebrew words.
Notice that in the first example even some Hebrew words have been split and in the second example more that one word often matches to a single word. This is common where suffixes or other grammar properties trace their meaning to different structures in each language.
This issue caught your attention because English is a left-to-right language while Hebrew is right-to-left, but actually it applied to all languages. For example if you look at a Greek-English interlinear some of the words will also be out of order, as will translation to almost any language.
Here's a subtle one from John 1:1, the ESV text with Greek interlinear:
Here is the same phrase in the Greek with English as the interlinear:
Note that translating any text involves more that just substituting words, you have to understand both languages and what structures connect the words to form meaningful relationships between them. Without knowing the language and just messing around with a dictionary, lexicon or interlinear tool you might well completely misunderstand what is even the subject vs, what is the object of the sentence.
The closer the languages are to each other in terms of language families the less pronounced this is, but even if both languages generally run in the same direction word order will not be the same. For example in English most sentences will commonly run subject-verb-object. In Turkish, sentences run subject-object-verb or in the case of using a pronoun for the subject, they are object-verb-subject where the subject is a suffix on the verb. As a result words get shuffled around if you try to show an interlinear almost as if the language was RTL (it's actually LTR). In fact the flow of thought is even more reversed in Turkish that many RTL languages where the sentence order is subject-verb-object even if it's written on the page in a different orthographic order.
And yes, most interlinears keep words as they are rendered in the original, so each even in the first example above the Hebrew words are read letter by letter from right to left of each word.