Well obviously like you mentioned it was a very complex process, and unfortunately there is no hard and fast rule to apply to any European Medieval City. All grew up in a maelstrom of shifting and differing circumstances.

But, enough with the platitudes about uncertainty. As you mentioned many of the larger cities had origins with the Roman Conquest of Britain, which brought larger populations and volumes of trade to the British Islands. While there is evidence that many cities were at least partially abandoned during the Sub-Roman period (once the Legions had departed and during the Anglo-Saxon invasions) many remained important trading and administrative centers. Perhaps most importantly, Roman fortifications remained intact at many, and only decayed over long periods of time. This meant that for the moment, Roman settlements offered unparalleled levels of protection to inhabitants of the local countryside during times of war, and represented key strongpoints during any conflict during this era. Once the Anglo-Saxons had established themselves as the ruling elite in the area we now consider England, they too were quick to take advantage of many Roman sites and their imposing fortifications.

One of the real ways in which English settlements started to make the change into more urbanised centers was during the reign of Alfred the Great of Wessex and the reigns of his successors. I've written on this before but Alfred began the process of instituting a program of defense based on Burhs - fortified towns garrisoned with local levies which were intended to lessen the impact and in some cases defeat the dangerous Viking raiding parties/invasions occurring in England at this time. Alfred began by primarily repairing and improving existing fortifications, in many cases utilizing existing Roman stonework such as at Exeter and London. In other cases he was forced to build defenses from scratch. But in any case this represented an unparalleled program of urbanisation alongside defense - as towns became safer, people were more likely to utilize them as avenues to sell goods, and their safety also encouraged various institutions to grow up in them. During this period the towns had a unique relationship with the King - in many ways they were independent of the shire in which they resided, especially in terms of taxation. But on the other hand they relied heavily upon the rural hinterland for troops to garrison them during wartime, and thus a precarious relationship evolved in many cases.

When the Normans took over the existing Saxon system of governance, they left much unchanged - especially in terms of local and geographical organization. Important urban centers such as London, where William built an important castle and where he was himself crowned, retained a special relationship with the King, and over time gained special rights and privileges that would be controversial in later reigns. New towns required a royal charter in order to be considered a city, and we have records dating as far back as 1066 of this process occurring. Edward I for example issued special charters to new colonial towns in Wales after its conquest in 1283 - this was an intentional move to bring in settlers from England.

Another example of a special relationship and position within the feudal hierarchy was the Cinque Ports - originally 5 port cities that were given special privileges in exchange for promising the support of a fleet during war time. This was for a long time the primary form of naval military organization for the King of England to call upon. While these cities were in some ways distinct from the shires they technically resided in, they were also overseen by a 'Lord Warden' by at least the 12th century, who had the distinct responsibility of overseeing their readiness and loyalty to the crown.

In sum, Feudalism in general was and is a nebulous concept that is currently being openly discussed in terms of its categorical legitimacy. Feudalism in England was anything but consistent, with some institutions and traditions remaining in place for centuries while others came and went. I would say that the city-making situation in England has heavy influences from all three distinct eras I discussed - Roman Urbanisation, the Saxon Burh system and Norman expediencies. I know that this didn't directly answer all of your specific questions but I hope it gave you a closer idea as to how the general picture looks.

Sources: Edward I by Michael Prestwich (1997) as always, just because of his peerless understanding of High Medieval Britain.

Frank Barlow's Feudal Kingdom of England, 1042 to 1216 is a fantastic (if dense) read that really goes in depth into how institutions changed and stayed the same during the transfer between Saxon and Norman administrations. If you are at all interested in this period I heavily recommend a read through.

Also, the article "Edward I, Builder of Towns," Medieval Academy of America, Caroline Shillaber is a shorter read and could give you a better idea of how towns were individually created and some of the special privileges they enjoyed, in this case referring specifically to those that Edward I created and maintained in Wales following the conquest in 1283.