Will Apple give me a hard time if I need to take my Mac in for some unrelated issue and I should therefore keep it and swap it back in should that need arise?
If you bought the product in the US, they legally cannot give you a hard time about it due to the Magnuson–Moss Warranty Act. Specifically, using 3rd party parts cannot void your warranty. Outside the US, check your local/federal laws specific to your country.
Where the Act applies to your question is with respect to using 3rd party parts. Specifically, they cannot "tie in" genuine Apple Parts (i.e. hard drives or memory) to keep the warranty in tact:
(c) Prohibition on conditions for written or implied warranty; waiver by Commission; No warrantor of a consumer product may condition his written or implied warranty of such product on the consumer’s using, in connection with such product, any article or service (other than article or service provided without charge under the terms of the warranty) which is identified by brand, trade, or corporate name;
The FTC has opined on this very question and I've written about it as part of an existing answer: Apple cannot void your warranty solely for using a 3rd party accessory. Note, "accessory" isn't limited to peripheral device like mouse or keyboard, but any compatible part like memory, hard drives, etc.
Can they try to give you grief about it? Sure. But that's where going in armed with the knowledge of what your rights are will help immensely. Further, speaking from a pragmatic side of things, all they (or you) have to do is simply remove the memory. Just because you bought it with 16GB of RAM doesn't mean you must take it in as you bought it - you can bring it in with 8GB (remove the 3rd party memory).
And again, speaking from a pragmatic point of view, the odds of more than one memory module failing at the time same time is very low. If a module fails you can remove the failed component and continue to function, so there's no need to keep backups of memory unless you're in a mission critical environment where uptime is key.
Standard disclaimer: I'm not a lawyer and definitely not your lawyer. Nothing written here should be construed as legal advice; it is simply my interpretation/opinion on this matter. If you need legal advice, seek out the services of an attorney in your area.