Are there geometrical differences between framesets optimised for flats vs drops, other than top tube length? Question background:
I am on the cusp of buying a 'do it all' bike for commuting and light touring.

The bike i'm looking at (Genesis Croix de Fer 2015 model) comes with drop handlebars. I would like to use a flat bar with a slight rise instead and bar ends.

I am aware that replacing drops with flats (in addition to requiring new levers and shifters) will change the handling of the bike somewhat. I can see that the most obvious way this would be will be a shortening of the reach, due to the extra forward distance from where a drop bar is clamped to the stem to the hoods/drops. Looking at frame geometries can also see that framesets for bikes with drop bars tend to have a shorter top tube to compensate for this.

My personal experience of riding most bikes is that I feel more stretched out than I would like to be, and I have test ridden the Genesis Croix De Fer and felt this to be the case. (I think I have a relatively short upper torso/arm reach).
I appreciate that a stretched out position is good for racing, but I would actually like a more upright position - this bike will be used for commuting and light tourer, and may one day take a child seat. I won't be racing on it.

Given this scenario, it seems to be that swapping drop bars that the bike is shipped with for flats (with a slight rise) may well make the overall geometry and riding position of the bike more suitable for my needs.

My question therefore, is, are there any other problems this will cause? e.g. will the handling be significantly adversely affected? 
I.E Are there ways in which framesets are optimised for drop bars OTHER than a shorter top tube, that I am not taking into consideration?
If the effective top tube (horizontal measurement) is OK for you - then the only other things I can think of might be the head tube angle &amp; chainstay length. A road bike may have a steeper head angle &amp; also have shorter chainstays. Which quickens the handling &amp; steering. 
Mind you, at the smaller end of the road bike sizing - the head angles tend to be a little slacker which helps with toe overlap. So head angle also depends on size.

Best thing to do is a compare a few geometries from a manufacturer for hybrid and road. There isn't a hard and fast rule for geometries. 

Also consider spacers as an alternative to a riser stem - might save you a few pennies.