Size may not be everything, but its very handy, especially in a mill where the extra rigidity pays.
Also you can as they say, do small work on a big machine, but you can’t do big work on a littl’un. But thats only true up to a point, because there comes a stage were larger equipment really does become unsuitable or unwieldy. But, within the normal span of modelling, bigger is usually better – more flexible for coping with future expansion? (Unless you are prepared to sub particular bits out, which is another option)
If you can afford it, or have the space, then go for the separate milling machine, just for the convenience and capacity. If you have difficulties, then do the modification. There will be limitations, of course, but mostly you will be able to make up for that with lighter cuts, resorting to jiggery pokery, and putting up with inconvenience. As long as, in general, the equipment is sized for the models or engineering you want to do.
I have no experience of working with the combi machine personally (and this is a combi machine of sorts), – clearly they are not ideal as mills, if only because the saddle gibs tend to be quite short and the x slide fairly narrow, relative to the loads when compared to a dedicated mill – nor is the bed as rigid.
However, for the person who has a bit of a space problem they represent a great gain in capacity. I saw a 5″ loco – quite a big model of a narrow gauge type, which had been (very well ) built on one. Passenger hauling all day having great fun. I think that the machine had been set up in a spare bedroom – indoors anyway. He couldn’t have built it without such a compact and flexible package, so who is to knock it in the circumstances.