I don't know if ETI will do customer counter trim but ChrisR of this forum used something similar; he did his own modifications. See here for his stunning work: https://escape440.wordpress.com/
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Karen Hulford
2013 Escape 15A, "Egbert"
'93 Ford 150 XLT or
'22 GMC Acadia Denali
I doubt that Escape would do either, but you could ask. The trim is not too tough, but they do need to limit their portions to keep production in line.
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2017 Escape 5.0 TA
2015 Ford F150 Lariat 3.5L EcoBoost
2009 Escape 19 (previous)
“Most folks are about as happy as they make up their minds to be.” — Abraham Lincoln
Depends on your definition of a skylight. Most skylights mount on raised curbs. Without a curb it would have to be surface mounted and would be more prone to leaks.
A marine rated hatch has a much stiffer frame and could be surface mounted with less risk of leakage.
Not likely that ETI would do that mod but within the range of an owner who really wants it.
I wouldn't expect Escape to install a different type of roof opening (such as a skylight) and take responsibility for it, but it might be reasonable to ask them to reinforce the desired area during construction as they do for other openings - but not actually cut the opening - then install it yourself (or have it installed) after receiving the trailer.