Why do some ---ify verbs have a different noun ending?

Solution 1:

Crucify originally had a distinct etymology from the others

Crucify comes from Latin crucifīgō with the present infinitive crucifīgere and the supine crucifixum. It means "to fix to a cross" not "to make into a cross". It ends in -fy in English because we got it through French; the OED says more specifically that it is from "Old French crucifier (12th cent.) = Provençal and Spanish crucificar, repr. a late popular Latin type *crucificāre instead of Latin cruci fīgĕre to fasten to the cross, subseq. as one word crucifīgere." Although this verb came to have the same ending as the other verbs you mention, it didn't originally, and the noun crucifixion remains faithful to its origins.

The verb suffix -ify comes from Latin verbs that had -ificat- forms

The English verb suffix -ify (which is moderately productive: you can see an overview of the tendencies for new formations at What is the difference between the suffixes -ize and -ify? and Suffixes for verbification: -ify, -icise, -ificate) comes from Latin verbs ending in -⁠ificō, an ending derived from a reduced form of the verb faciō "make". Latin verbs ending in -ificō belonged to the first conjugation and so had present infinitives ending in -ificāre and past supines ending in -ificātum, with the thematic vowel A.

Some potential -ification nouns are "blocked" by other nouns

Testify seems to be from Latin testificor which basically just conjugates like the passive form of an -⁠ificō verb, as it is a first-conjugation deponent verb. It has the participle form testificatum.

The word "testification" exists in English, it's just very uncommon. A well-established preexisting noun related to a verb will usually be preferred over a more complicated noun derived from the verb that would have the same meaning; this is called "blocking", and there are other examples like how *terrification and *horrification are very rarely used compared to terror and horror. Aside from blocking by testimony, another thing that might play a role in the low frequency of "testification" is that the meaning of the suffix -ify seems to be somewhat more opaque in testify than it is in some other words ending in -ify.

The -(i)faction nouns are based on the conjugation of Latin faciō

Satisfy comes from Latin satisfaciō, which conjugated like faciō in Latin as a third-conjugation verb without vowel reduction. The present infinitive was satisfacere and the supine was satisfactum.

There are a number of nouns aside from satisfaction that end in -(i)faction and are related to verbs ending in -(i)fy. See the results for *ifaction on OneLook Dictionary Search. One example is putrefaction (corresponding to the verb putrefy), which seems to be much more common than putrefication. Some other examples are petrifaction (corresponding to the verb petrify) and liquefaction (corresponding to the verb liquefy).