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The word domus is normally a feminine, IVth declension noun and hence the adjectives that modify it are feminine.
However, sometimes domus appears to take masculine forms in some cases. For example, we have the "Comes Domorum" (the count of the houses), who was the official in charge of the imperial palaces. Likewise, the ablative domo and plural accusative domos are also found. What is the explanation for this? Why would domus have these gender-irregular forms?
In Old Latin domus (then domos) was usually declined as a second-declension noun, though it was feminine even then. It's probably the case that it was shifted into the fourth declension in an attempt to make its unusual gender make sense—so it's not the retained second-declension forms that are unusual, it's the new fourth-declension ones.
This actually happened to a greater or lesser extent for a lot of feminine second-declension nouns: e.g. nurus 'daughter-in-law' has fully joined the fourth declension (cf. its Greek cognate νυός, still a second-declension feminine), while fagus 'beech' and laurus 'laurel' are still in the second declension but also have an attested acc. pl. in -us. Feminine second-declension nouns seem to have confused Romans nearly as much as they confuse students today. (Conversely, quercus 'oak' is a native fourth-declension noun that has an attested gen. pl. quercorum.)
For domus, this shift was already underway in Old Latin, and pretty much completed in Classical Latin, apart from the occasional now-irregular form and archaism.
As for why domos was feminine in the first place, that's less clear. We can reconstruct perhaps three basic Proto-Indo-European words built on the root *dem- in the o-grade meaning 'house' based on reflexes in daughter languages:
PIE o-stems gave rise to Latin's second declension and u-stems to its fourth, but as domus's membership of the fourth declension seems to be an innovation we can disregard influence from PIE *dómus (which is certainly masculine anyway). PIE o-stems in *-os were overwhelmingly masculine, and the Greek and Sankrit seem to confirm *dómos was too; by rights a Latin domus inherited from PIE *dómos should be masculine.
The gender of PIE athematics is less predictable (much like the Latin third declension, into which most of them went), and it's very inconvenient none of the high-profile reflexes of *dṓm is feminine. Mainly on the strength of Latin (!), *dṓm is still usually taken to be feminine, though, and if that's assumed, then Latin domus could have retained its feminine gender from it, after it either merged with *dómos or (in my view more likely) independently became thematised (in which case it effectively hopped declensions from the third to the second to the fourth over the centuries).
Some sources worth your time (though they don't say anything else that's relevant here, I don't think):
Genitive plural domōrum, ablative singular domō, and accusative plural domōs aren't masculine forms, they're second-declension forms.
It's true that most first-declension nouns are feminine and most second-declension nouns are masculine or neuter, but this is just a rule of thumb. Declension isn't necessarily linked to gender: nauta "sailor" is masculine, and quercus "oak" is feminine, for example. So a good sailor is a nauta bonus, and a good oak is a quercus bona, and good houses in the genitive plural are domōrum bonārum.
Although domus may look masculine, it's a feminine noun through and through — that is, there are no masculine forms, as you say.
According to Latin Grammar by Allen and Greenough:
90. Most nouns of the 4th Declension in -us are masculine.
Exceptions:
The following are feminine:
acus, anus, colus, domus, īdūs (plural), manus, nurus, porticus, quīnquātrūs (plural), socrus, tribus
with a few names of plants and trees. Also, rarely, penus, specus.
From the Latin Grammar:
Grammatical Gender is a formal distinction as to sex where no actual sex exists in the object. It is shown by the form of the adjective joined with the noun.
In other words, gender is not tied to the declension or how the declension might appear to you, but to the adjectives joined with it.
Therefore, in spite of appearances, domus is feminine:
| Case | Singular | Plural |
|---|---|---|
| Nominative | domus | domus |
| Genitive | domus/domi | domorum/domuum |
| Dative | domui/domo/domu | domibus |
| Accusative | domum | domus/domos |
| Ablative | domu/domo | domibus |
| Vocative | domus | domus |
| Locative | domi | domibus |
In your example, Comes Domorum, there is no adjective involved — just the noun itself Domorum which is feminine. The same is true of domo, domos — all are feminine.
We don't exactly know why domus has both second and fourth declension forms, but one possibility is that there were originally two separate words that merged, perhaps because a feminine second declension domus is unusual. It's also possible that there was only the o-stem and over time Romans used fourth declension endings for it, for the same reason as above.
From De Vaan:
In PIE, there was a root noun nom.sg. *dōm, gen. *dem-s. Probably, a u-stem derivative also existed (yielding Slav. *domu- 'house' and Gk. δμώς 'slave' < **dm-ou-).
...
The f. gender of domus probably is due to the original root noun. Old Latin mainly has o-stem forms; the change into a u-stem which some case forms show may be explained from an attempt to adapt the declension type of domus to its f. gender, which is unusual for Latin o-stems (apart from tree-names).
