I suppose it could be different in other regions, but for me, those are two different sounds. I would pronounce it as /e'ɛ/. There is some kind of subtle-ish stop between the two words, but it can be difficult to catch.

As far as how I speak, “et” is pronounced like a canonical “é“, whereas “est” is the canonical “è“. This however may not mean much in certain parts, as certain regions and accents have a tendency to erase these differences, see « Patte » contre « pâte » : qui fait encore la différence ?

I pronounce both et and est exactly the same way /e/, however, to avoid that hiatus I would have written that sentence :

Ce projet a commencé comme un fork de Node.js™ de Joyent et il est compatible avec l’écosystème npm.

My answer is that together, these words would sound like Elêt. Although I am not 100% sure about it.

I wouldn’t put a glottal stop, or even a pause between those two words. Trying to pronounce it I find I either just make the vowel twice a long, have a slight dip in sound intensity between the two (not a glottal stop, more like a tapering off of the first vowel and then start of the other before the tapering’s done), or a natural change in tone between the “et” and the “est”, of the kind of have between different parts of a sentence.