Here is what the CFTDI says for inside the HQ area:
5.10 Meals
(1) Meal expenses incurred within the HQ area shall not normally be reimbursed. Each unit must provide a lunch break approximately midway through the regular work period or shift to enable each member to obtain a meal at their own expense.
(2) If the CO considers meal expenses during normal working hours as reasonable and justifiable, a member on TD within the HQ area is entitled to be reimbursed actual out-of-pocket expenses, based on receipts, up to the limit of the applicable meal allowance in Appendix C of the following Treasury Board website, http://www.tbs-sct.gc.ca/pubs_pol/hrpubs/TBM_113/td-dv_e.asp, provisions of CFAO 36-14 still apply. The following are examples of when meal expenses may be reimbursed IAW the meal hours listed at Section 6.10 paras 2 and 3:
a) when members are required to work through normal meal hours as approved by their supervisor (this primarily refers to lunches, however, breakfast and dinner may apply on rare occasions). A reasonably delayed meal hour does not create an entitlement to a meal at Crown expense;
b) when members are required to attend conferences, seminars, training sessions, meetings or public hearings during the weekend or holidays, where meals were not provided by a third party;
c) when members are required to attend formal full-day conferences, seminars, training sessions, meetings or hearings, and meals are a required part of the proceedings;
d) when members are on ration strength but because of an absence on authorized duty are unable to take a meal at the mess and have not been provided with a box lunch; or
e) when members are required to work outside the primary work place, and their participation in an intensive task force or committee work is enhanced by keeping members together over a normal meal period.
And for outside the HQ area:
6.10 Meals
(1) A member is entitled to be reimbursed the applicable meal allowance rates set out in Appendix C of the following Treasury Board website, http://www.tbs-sct.gc.ca/pubs_pol/hrpubs/TBM_113/td-dv_e.asp, for each breakfast, lunch and dinner while on TD. A meal allowance shall not be paid to a member with respect to a meal that is provided by a third party or other government agency. Members shall only claim for those meals that they were not provided.
(2) A member is entitled to be reimbursed the applicable meal allowance for each breakfast, lunch and dinner provided that:
a) for breakfast, the member must depart from home on duty travel before 0630 hrs;
b) for lunch, the member must be on travel status between 1130 hrs and 1300 hrs; and
c) for dinner, the member must arrive at home after 1800 hrs.
(3) A member who is on duty between 1900 hours and 0730 hours for four hours or greater is entitled to be reimbursed, with receipts, actual and reasonable expenses not exceeding the amount payable for a lunch, for a single night meal, when the CO considers that the purchase of the meal was necessary to ensure the proper performance of the duty.
(4) Reimbursement of meals for shift workers shall be based on the meal sequence of breakfast, lunch and dinner in relation to the commencement of the CF member’s shift.
In short, the answer is yes, but there are caveats depending on the circumstances. Note that there is no mention of whether the member is on IR or not (i.e. no exclusion) and if this is an occasional issue, as a comptroller, I wouldn't bother trying to adjust SE. Keep in mind that SE assumes you are eating at home (well, second home in fact) and/or brown-bagging it. This is not the case when on travel status. However, if this is a regular occurance, then I would look at it differently.
