Hoe laag die saal ook al is, kan ons dit verstel.

It is a common Afrikaans pattern meaning however low or no matter how low.

So:

Hoe laag die saal ook al is
= No matter how low the saddle is

More generally, hoe + adjective/adverb + ... + ook al expresses concession: something is true regardless of degree.

For example:

Hoe moeilik dit ook al is = No matter how difficult it is
Hoe vinnig hy ook al hardloop = No matter how fast he runs

By itself, hoe often does mean how.

But in this structure, hoe ... ook al, it means however or no matter how rather than asking a question.

Compare:

Hoe laag is die saal? = How low is the saddle?
This is a real question.

Hoe laag die saal ook al is, kan ons dit verstel.
This is not a question. It means However low the saddle is, we can adjust it.

Ook al is a fixed expression in patterns like this. It gives the sentence the sense of no matter, even if, or however.

It does not mean also already here, even though the words separately can have meanings like also and already/all.

In this sentence, ook al helps create the idea:

hoe laag ... ook al = no matter how low ...

You will see the same thing with other words:

wie ook al = whoever
wat ook al = whatever
waar ook al = wherever

Because hoe laag die saal ook al is is a subordinate clause.

In Afrikaans, the finite verb usually goes to the end of a subordinate clause.

So the order is:

hoe laag + die saal + ook al + is

That is why you do not get:

Hoe laag die saal ook al, is ...
or
Hoe laag is die saal ook al ...

The final is is normal subordinate-clause word order.

Because the sentence starts with the subordinate clause.

Afrikaans main clauses normally follow a verb-second pattern. If something other than the subject comes first, the finite verb comes before the subject.

So:

Kan ons dit verstel
not
Ons kan dit verstel

Here the first position is already taken by:

Hoe laag die saal ook al is

After that, the main clause begins with the finite verb kan, and then comes the subject ons.

Because laag is being used predicatively, not directly before the noun.

Compare:

Die saal is laag.
Here laag comes after the verb, so it stays laag.

die lae saal
Here the adjective comes before the noun, so it usually takes -e.

In your sentence, the structure is like the saddle is low, so laag is correct.

Dit refers to die saal.

So:

kan ons dit verstel
= we can adjust it

Afrikaans often uses dit for an inanimate thing like a saddle, seat, device, object, and so on.

Here verstel means adjust or change the position/setting of something.

So ons kan dit verstel means:

we can adjust it

This is a normal verb for things that can be moved or set differently, such as a saddle, seat, mirror, or machine setting.

Not if you want the same meaning.

Without ook al, you lose the no matter how idea. The sentence would sound incomplete or would no longer clearly express concession.

So:

Hoe laag die saal ook al is ...
= No matter how low the saddle is ...

But:

Hoe laag die saal is ...
does not naturally mean the same thing.

Because the sentence begins with a subordinate clause, and then the main clause follows.

So the comma separates:

Hoe laag die saal ook al is,
from
kan ons dit verstel.

This is standard punctuation in Afrikaans.

Yes. A common alternative is:

Maak nie saak hoe laag die saal is nie, ons kan dit verstel.

That also means:

It does not matter how low the saddle is; we can adjust it.

Your original sentence is slightly more compact and elegant, but both are natural.