Note that I'm answering this from the perspective of an applicant rather than someone on a PhD admissions committee.
"(...) how would having one of those degrees affect an application as opposed to having a standard degree in physics?"
I don't think that the name of the degree itself would affect your application. However, I think it would be a good idea to make sure that you carefully explain the content of your degree (for instance, in your research statement/ statement of interest/ personal statement, or get one of your referees to do this in their letter), so that the admissions committee understands what courses you have taken and how these relate to a more "standard" degree scheme.
From the degree titles that you mention, I'm guessing that these will involve a large amount of normal undergraduate physics and maths, the names of which will also be on your transcript for the admissions people to see.
"I'm also worried that such novel degrees would spark cynicism and
distrust that could be disadvantageous to a potential application for a PhD."
The most important component of a successful PhD application is your demonstrated aptitude or ability to perform research. If you can do this, and do it well, then I think the name of your degree will matter less.
I speak from personal experience on this; my undergraduate degree is in Astrophysics, with a lot of specialised astro modules, but for my PhD I'm moving into theoretical cosmology, an area which is more commonly populated by applied mathematicians and theoretical physicists. I just had to make sure I "sold" my degree to the admissions committees by explaining that my degree was sufficiently theoretical. Getting some research experience by writing a dissertation during my fourth (Master's) year undoubtedly helped this.
If you're still worried about people distrusting the value of your degree, I would recommend trying to find out if the degree scheme is accredited in any way; for example, here in the UK, all reputable physics degrees are standardised and accredited by the Institute of Physics. I don't know what country you are in, but something similar may exist there.
Finally, as I mentioned in a comment, it might be best not to specialise too early (although you sound as though you have a pretty good idea of what you want to do). The option in this case would be to enroll on a straight physics degree scheme and specialise later on by taking any optional modules that are available (modules which would probably be mandatory if you were on the Quantum Engineering scheme, for example). The best person to advise you about the possibility of doing this would be the admissions tutor at the university offering these courses. They will be able to tell you what combinations of modules lead to which degree.