Any syllable that ends in a consonant (one or more) is heavy
The terms "length by position" and "length by nature" are often avoided in more modern work. It's better to speak of "heavy syllables" and "light syllables". As described in the answers to a previous question, What makes a syllable "heavy" or "light"?, if you follow a certain system of syllabification, then a light syllable can be defined as a syllable that ends in a short vowel.
I think you may have misunderstood part of the second rule in the quote. The wording "If the syllable contains a vowel which is followed by two consonants" may be confusing: for the purposes of this rule, the two consonants mentioned do not both have to belong to the same syllable as the vowel. It is sufficient for only the first consonant to belong to the same syllable as the vowel.
In the middle of a word, most sequences of consonants are divided between syllables in Latin, and so most sequences of consonants cause a preceding syllable to be heavy. For example, pango, stultus, discus all start with heavy (="long by position") syllables: pan, stul, dis. Doubled consonant letters in Latin represent doubled (or "geminate") consonant sounds, which are also divided between syllables, as in passus, siccus, terra, which start with the heavy syllables pas, sic, ter.
The only consonant sequences that are not always split between syllables when they occur between vowels in the middle of a word are two-consonant clusters where the first consonant is one of P T C B D G F (PH TH CH) and the second consonant is one of L R. It is possible for both consonants in a cluster of this form to be grouped with the following syllable, so for example the word tenebrae has the syllabification te.ne.brae, and also an alternative syllabification te.neb.rae. The syllabification of such consonant sequences in poetry is somewhat free, which can enable the poet to use a heavy or light syllable depending on the requirements of the meter, but there are certain restrictions, or conditions that make one or the other syllabification more likely. I'm not sure whether you want the details, but the most definite restriction that I know of is that any cluster formed by adding a consonant-final prefix to a base starting with L or R is split between syllables (so a word like oblītus started with two heavy syllables, ob and lī).
Aside from X, there are a few more cases where Latin spelling represents two consonant sounds with just one letter. The most important are J (also written I) and Z: when these occur between vowels in the middle of a word, they almost always represent doubled consonant sounds /jj/ and /zz/, which were divided between syllables just like other doubled consonant sounds. So for example, major/maior, which was really pronounced majjor, starts with the heavy syllable maj.
Syllabification in multi-word sequences
When a word ending in a consonant came before a word starting with a vowel, Latin speakers regularly moved the word-final consonant to the start of the following syllable, so the first syllable in ad rem is long (/ad/) but the first syllable in ad oppidum is short (/a/), since the phrase is divided into the syllables a.dop.pi.dum. Likewise, a single consonant in the middle of a word was grouped with the following rather than the preceding vowel. This is why traditional sources often phrase the rule of heavy ("long by position") syllables in terms of a vowel being followed by at least two consonants.
For consonant sequences at the start of a word, both consonants are generally grouped with the following syllable, even when the preceding word ends with a vowel, so a phrase like sine prōle would normally be syllabified as si.ne.prō.le, where the second syllable is light. But I believe I've read that the situation is less clear for word-initial consonant sequences that start with S, such as st sp sc str.
Long vowels and short vowels still contrasted in closed syllables
The reason for calling heavy syllables "long by position" is because syllables with long vowels and syllables ending in consonants were treated the same way in Latin poetry. Latin poetry has rules for which syllables in a line should be heavy and which should be light.
There was still a distinction between long and short vowels in syllables that ended in a consonant. For example, the word āctus had a long vowel /aː/ and the word factus had a short vowel /a/.The distinction just didn't make a difference to the behavior of the syllable in poetic meter: "āc" and "ac" are both heavy syllables. You should not pronounce a vowel as a long vowel just because it occurs in a syllable ending in a consonant.