Thank you all, particularly aldebrn, for your help!
here is the list I'm using, I've covered up to 80% and for the most part those are common words found also in Core 10000, but with different priority (words that core puts as most frequent aren't found until late in the novel frequency list, and viceversa). So in the end I just suspend words in Core 10000 but following the novel frequency list order.
Most of the words not found in Core are:
1) hiragana words, a bunch of them, like conjunctions etc.. maybe used on literary style but not on newspapers?
2) words like 警部, 斬る, 江戸;
As for 2) those are very few, I went from 0% to 79% of the novel frequency list and end up adding only 15 new kanji compounds, while the other were already on core 10000.
As for 1) from 0% to 78% I've found those which are not present in core 10000 (I didn't check them all so I'm not sure they are all true words or not):
90317 けれど 0,02469785 66,09529207
82298 こそ 0,02250500 66,82698427
81543 わし 0,02229854 66,84928281
77866 なり 0,02129304 67,24128128
76125 とも 0,02081695 67,45242376
75459 まい 0,02063482 67,55586094
72033 いける 0,01969796 68,01986540
64289 しかも 0,01758030 68,87128300
59459 がる 0,01625950 69,48067191
48619 あるいは 0,01329523 71,02959788
48461 いえる 0,01325202 71,06942066
44041 つて 0,01204334 71,69093987
42981 それも 0,01175347 71,88111474
36474 とともに 0,00997409 73,27073372
36204 において 0,00990025 73,32040644
35353 かく 0,00966754 73,53517688
34986 こうして 0,00956718 73,63136662
34727 つぶやく 0,00949636 73,68847328
34513 むしろ 0,00943784 73,72629244
34502 さすが 0,00943483 73,73572727
33885 ごと 0,00926610 73,95067163
31633 それとも 0,00865028 74,46094399
30027 それだけ 0,00821111 74,79055397
27865 なお 0,00761989 75,41494804
27200 それら 0,00743804 75,60305666
24804 すら 0,00678284 76,33250760
24606 そりゃ 0,00672869 76,41353714
24461 それにしても 0,00668904 76,44034198
23950 ほら 0,00654931 76,59252076
23133 ずつ 0,00632589 76,79804616
22671 こうした 0,00619955 76,92313269
22637 そこから 0,00619026 76,93552140
22549 ものか 0,00616619 76,96640896
22432 そうした 0,00613420 77,00328278
22030 やら 0,00602427 77,10665515
21749 それより 0,00594743 77,21439956
20486 それでは 0,00560205 77,61857291
19861 ほんの 0,00543114 77,86105908
So from this I can say that, at least up to 80% coverage, the novel frequency list share a great amount of words with core 10000. But in the end they are only 1800 words. Less if you exclude things like 僕、ぼく、ボク are treated as three different words. And things like adverbial forms of adjectives, or some conjugations, are treated as words per sé.
I wonder what happens in the next 6000 words circa, from 80% to 90%. How many of those words are also in core 10000?
But one thing is sure, if your main goal is to read novel it's better, at least for the first 2000 - 3000 words or so, to not follow the core 10000 order. Or when you'll reach 2000 words in core 10000 you'll find yourself with many words maybe commonly used in 90's newspapers but not so much common in novels.
Another thing I wonder is, from what coverage words begin to be more specific and it's better to just put apart computer made lists and just use the books himself as your list, i.e. adding new words as you encounter them in reading.
I think from 0% to 90% if you study them from a list you're sure your time is well invested. But maybe from 90% up to 95% and on, altough those are still common words you'll need to know before or after, it's better to study them as you encounter them so you'll know first the words you effectively need to know to just continue reading what you're reading. Words like "私立" as in "private investigator", given as 93% from the novel frequency list, but useless to study a priori from a list if you're going to read only fantasy novels for the next six months. Or viceversa, very useful if you're going to read "death note another note" but in that case it's meaningless to study words like "使い魔" which is very common in fantasy novels but rarely usel on thriller novels.
So what do you think? From what percentage of coverage words become less general and more specific to not justify the need to study them from list? Like up to 80% I've seen they are all very useful and generic words you'll surely encounter whatever you'll read.