<p>Dear OP,</p>
<p>I don’t think applying to MS-only will hurt you. Note it also says that:</p>
<p>Applicants to the M.S.-only program are considered separately from those applying for a Ph.D. </p>
<p>Therefore, if what you want is an MS and NOT a PhD then do the MS-only program. But, if you plan to eventually go on and do PhD, then you should apply to the PhD. </p>
<p>I think it infact is easier to get into the MS-only program, especially based on what was said above (ie not being considered alongside other PhD applicants). </p>
<p>Best wishes,
-DV</p>