Regarding your first question, in the body of text there is no confusion when applying boldface since the literary boldface indicator is not used in a Nemeth transcription--the Nemeth boldface type-form indicator would be used. If italics are retained for the two examples you cite, "Cos" is an abbreviated function name (mathematical) and so the Nemeth italic type-form indicators should be used. "Parallel" is a word and so the literary emphasis indicator should be used.
Next you ask about linked expressions. A linked expression is defined in the Nemeth Code in Section 189a, portions of which are copied below (in quotes) with comments added by me (in brackets).
"A linked expression must contain at least one sign of comparison." [Note that the equal sign is not the only sign of comparison.] "The component which precedes the first sign of comparison is called the anchor." [So, yes, in order to be a linked expression there must be an anchor.]
A linked expression is not necessarily vertically arranged. IF it is vertically arranged, and IF it follows the other print criteria stated in NC Sec.189b, then the special braille format is applied. The example you provide has anchor so, by definition, it is not a linked expression. The text "The hypotenuse equals:" is simply the last phrase in the itemized paragraph. The layout of the five displayed expressions will be 5-7 (displayed material to 1-3) although runovers are not indicated in this example.