Yes, it makes sense...it would be "strange" if Otto, one of the most important members of the Imperial Family, head of the Family for 85 years, will be buried in the grave of his parents in law.
And maybe Archduchess Regina will be buried in Veste Heldburg in order to celebrate her funeral in a short time; I mean, Archduke Carl Ludwig's funeral was celebrated 32 days after his death; maybe due to the bureaucracy, to get the necessary permission to bury him in the Kapuzinergruft? Maybe because they needed time to prepare the crypt and his grave?
I don't know the reason of this large period of time from his death to his funeral; but if it was due to something unavoidable for bury him in the Kapuzinergruft, it's also possible that Archduke Otto and his children have decided for the temporary burial in order to cope with the bureaucracy or whatever else is with calm and less pressures.