I prefer not to use the term "command" in referring to the pre-commissioned activities of Clagett (Elcon Jones, and the others), but use "in charge" or other "non-official" descriptive term for that brief period. Note, too, that GO 10, A&IGO 24 Jan 1863, ordered that only men with commissions in the Sig Corps were to be recognized as sig officers. (This was not rigorously enforced, but causes various snarls with AG commissions, etc.)
As to commission dates, I know you're familiar with the various stages of the commissioning red tape and the important "to rank from" dates. I try, when I can secure the info, to use the official date of commission which formed the basis for resolution of pecking order if two officers had to compare for command purposes. (Recall how important that little factor, as well as line/staff, was in movie "Zulu.") I have these dates for a few of the Sig Corps officers and sgts, and, in Capt. Clagett's case, it is 29 May 62, which agrees with the date in your CSR holdings and is the date of GO 40, A&IGO, which implemented the law. (Just as a general note, resolution of seniority in the Sig Corps appears to have been alphabetical by surname for those bearing commissions of the same date, and a master numbering -- "pecking order" -- was kept to conform to the statutory imitations -- originally ten officers not to exceed rank of captain and ten sig sgts, twenty men in May 1862. In Sep 62, more billets were added to increase the authorized size, by adding one major, retaining the ten captaincies, but adding ten first and ten second lieuts, plus twenty ADDITIONAL sergeancies, making thirty sig sgts, a total of 61 slots. No pvts or corporals, except through details. M258 fails to distinguish the official Sig Corps, PACS, from the detailed men except where that info is reflected in reading the indiv CSRs, and, in turn, lumps in the men of Milligan's "Independent" signal corps, a practice continued in Bob Driver's 2007 compilation of signalmen from Va and Md.) Just to explain where I'm coming from in my reasoning.