I don't pretend I am clever enough to have any in-depth dialogue in this particular department but curiosly : Does still containing their own DNA becoma a hindrance somehow? Mitocondria and cloroplasts seem to be functioning and working quite well from your discription of the two.
Original design flaws according to: the "believed to have started out "theory". Only just recently in our own time we realised "junk DNA" is not actually junk DNA after all. Having our appendix removed not-so-long-ago with the "belief" that the appendix was a useless part of the anatomy ... a previous flaw designed argument no doubt , and in fact it was later realised in our lifetime , the appendix is part of the immune system.
I don't think you understand what is being discussed. Free living (prokaryotic) bacteria were assimilated into prokaryotic organisms to form endosymbiotic systems, and this happened billions of years ago. All complex organisms today use cells that evolved from these basic prototypes. The systems that evolved were more efficient at performing certain cellular functions like providing energy, using radiant energy to build sugars etc than the original prokaryotic cells that existed before the formation of the eukaryotic cells. This is not to say that the eukaryotic cells are perfect, they are not. The way even modern eukaryotic cells get energy from food is complex and involves many convoluted steps. If you were to argue that living cells were designed by an intelligent entity, you would have to explain why:
1. a designer would first design prokaryotic cells, than change his mind 500 million years later, and inject some prokaryotic cells into other prokaryotic cells to form the first eukaryotic cells, and
2. why the energy producing mechanism in even modern eukaryotic cells are so unnecessarily involved and inefficient, i.e. NOT intelligently designed.
And while you are at it, you might want to explain why human and chicken embryos, among many others, start off with gill arches. Or why whales live in water but have lungs, and some of them even have small vestigial legs. Or why God created at least a dozen human-like species in the last 6 million years before he got to us, and then killed them all off. All of these things are explained by evolution, but are absurd in the context of an intelligent designer.
The much more reasonable explanation is that there is no intelligent designer involved, that modern eukaryotic cells evolved from older less sophisticated cells, and while they get the job done, they are not perfect. Which is how evolution works.
Sort of what Lion highlighted
The gap is where you insert the word "spontaneous" instead of "cause(s) unknown".
...unlike in biblical theism where God is the known cause. (No gap to fill.)
Theists don't KNOW that God is the cause; theists BELIEVE God is the cause. Big fucking difference! Theists don't have a lick of evidence to support their beliefs other than some stories written 2,000 years ago. Saying Goddidit doesn't actually answer real questions, it avoids them.
Example: Why is the sky blue?
Theist: Because God made it blue
Scientist: The sky is blue because certain portions/wavelengths of the light spectrum reaching the Earth gets scattered by dust and moisture in the atmosphere, and these wavelengths correspond to the part of the color spectrum we call blue.
There is no "spontaneity of the gaps", that was just Lion trying to be glib. Lion is glib a lot, but he almost never has anything factually meaningful to say.
Example: (a) I don't know who ate the last cookie. (b) Therefore, God ate last cookie.
(b) does NOT follow from (a).
Meanwhile, we are still waiting for LionIRC to step up and tell us how God turned rocks into living things. He wasn't just making up shit when he said he knows this, right? Right?
...unlike in biblical theism where God is the known cause. (No gap to fill.)
Go on, fill in the gap. 
