The two manuscripts read chose. However, the manuscript spelling could be a misspelling for choose since Oliver Cowdery typically spelled choose as chose in the manuscripts (see under the Words of Mormon 1:4–6 for a summary of the evidence). Here in Alma 40:13, the 1830 edition reads chose, but the 1837 edition reads choose. This change from the past-tense chose to the presenttense choose may have been influenced by the use of the present tense in the preceding text: “the spirits of the wicked—yea which are evil—for behold they have no part nor portion of the Spirit of the Lord”. The change in the 1837 edition may have been unintentional; it was not marked by Joseph Smith in 𝓟. The RLDS text has retained the present-tense choose, but the 1879 LDS edition restored the 1830 chose, undoubtedly because the past tense in “they chose evil works rather than good” works better with the following text: “therefore the spirit of the devil did enter into them and take possession of their house”. The preceding present-tense are and have refer to the future state of the wicked, as is described later in this verse when Alma returns to describing what will happen to the spirits of the wicked, those who chose evil works in this life: “and these shall be cast out into outer darkness / there shall be weeping and wailing and gnashing of teeth”.
Summary: Maintain the past-tense reading, chose, in Alma 40:13 since here Alma is referring to why the spirits of the wicked are evil: namely, they chose evil works in life.