I understand I may not be admitted into the USA based on the fact a current visa application is underway.
A pending visa application is no bar to admission in a different status. The problem with the pending visa application is that it may imply some fact that is inconsistent with the other status. In particular, to visit as a "visitor for business or pleasure" (that is, in B-1 or B-2 status, or through the visa waiver program), you must have no intent to immigrate, and your pending application for an immigrant visa indicates an intention to immigrate.
This isn't as much of a problem as it might seem, because as long as you do not intend to immigrate during that particular visit, you can be admitted as a temporary visitor. Still, it's wise to proceed with caution because an immigration officer can always decide that you haven't been sufficiently convincing -- they might see your pending application to immigrate and infer that you are trying to shortcut the process.
But that's not what you're asking about; it is just context.
if I am refused entry into the US, does this affect my chances of securing my future green card?
This depends on why you were refused. If you are refused for using deception, for example, or because of something else that implicates grounds of inadmissibility, then yes, it could well affect your application for an immigrant visa. However, if you are refused admission because you are found to have immigrant intent, that will not affect your application to become an immigrant, because of course an applicant's intending to immigrate is not a reason to refuse an immigrant visa.