First question... Kinda obvious but I have to ask... Is that an Integra? If so, great. If not, if it's just a straight Compact 406AF, then you don't have an internal antenna to worry about.
(Apologies for being Captain Obvious, but in truth I have answered this question before in conversation with another builder, only to realize he didn't have an Integra with its built-in GPS antenna!)
As much as I hate to say it, neither mounting proposed mounting location is particularly good, for the reasons you've already pointed out. The baggage area is an area where the contents get squished, bashed etc in day-to-day use. The wiring will get snagged and yanked. The switch will get crushed. Every time I see an ELT mounted in the baggage compartment I cringe. I also cringe because I've seen inadvertent activations because something snagged a switch and turned the unit on.
If you really want to install an Integra it might be worth considering making a bracket for it high up in the turtle deck area just aft of the baggage bulkhead so it is close to the skin, then fabricate a doubler ring for the skin and install a composite "window" much like an inspection panel to allow the GPS antenna a view of the sky. I don't have the capacity to determine how big the doubler ring would have to be to support the installation of something like a 4" square composite "window"... Seems like a lot of work.
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