Yes it can - in fact I read this somewhere. If stress acts on your gut - which it does, then it will affect any medication that you take. If it means faster transit than usual then you could absrob less. This is why oral meds can give a more variable result - certainly this is the case with HRT.
Just had a look at the paper I have on this.
This is from the section about pharmacokinetics of oestrogen ( ie what happens to it in the body after it's taken in):
Owing to the large individual differences in the resorption and metabolism, there are considerable interindividual variations in the course and height of the serum concentrations of sex steroids in women treated with the same preparation. The coefficients of variation are usually in the range between 30 and 60%. The interindividual variations are mainly due to genetic or acquired differences in the intestinal and hepatic metabolism, while the intraindividual variations from day to day may be caused by external factors like diet, alcohol or drug consumption, smoking, physical activity, stress, etc., which may cause rapid and transitory changes in peripheral or splanchnic blood flow, absorption or metabolism
The paper is "Pharmacology of estrogens and progestogens: influence of different routes of administration" Kuhl 2005
Hurdity x